I'm specifying private server since some of the bugs here are definitely private server related, like the map bug thing. I have no idea whether all of them are, but just in case! Also you may have fixed some of them already, but due to the first thing on the list, I'm afraid I can't get back in to test more.
* Most recently, cannot rejoin server. We were kicked out of the server trying to cross the barrier between the main server and an expansion server, and since then we haven't been able to rejoin. We were playing version 5 on the server, the game's title page said that 5.2 was coming soon, but I was somehow playing version 5.3. Everything's synced up to 5.9 now, but still can't enter the server, even after reinstalling it and wiping all files on both the main and the expansion. (May be a Nitrado thing; I've reported this to them, too.)
* While in the private server, our maps don't seem to work. Instead of what I'm seeing in screens and vids from official players--an actual map once the FoW is removed--we just have this solid block of grey fog that never lifts. We can see what might be rocks? and a skull in a triangle? as markers on the map, but we just have to sort of shoot for them blindly. Not being able to see the shape of the islands as they're uncovered is going to make the treasure map minigame pretty much impossible. There was also a point while we were heading for the cell border and passed an island that was north of us but which definitely should have been south of us--we can see the X of our position, and the only landmark that fit the bill was definitely not in that location, so...maps seem really, really buggy on our server right now. Can't retest it at the moment, though, sorry.
* Beds do not work for me. They might possibly work for my friend, but even after placing one down, I'm unable to spawn there or see it on the fast travel options screen. The fast travel options screen is also just a plain black box without a map. I also can't see the bed she placed, even though she made and placed it after we created a company. The company log registers that we've added beds to the company, but so far they're unusable. Might be a server thing since the map seems to be buggy here too, and I recall seeing a map of bed locations when I fast traveled or spawned in Ark.
Probably Not Server-Related
* Adding weapons to your hotbar is really strange...? This is going to be hard to describe, but basically if you have no weapons on your hotbar and want to add one, you can add it to any slot. However, once you've added a weapon to your hotbar, if you want to add another weapon, you pretty much can only replace the one that already exists. I've seen people who play on officials commenting that they can't equip their fishing rod, and then that they can only equip it where their spear was, which sounds like the same problem. Say I have a spear and want to add a bow. The bow can only go where the spear currently is--I can't have a bow and a spear equipped on my hotbar at the same time. Same goes with fishing rods, as they're considered a weapon. I can have a spear/bow/fishing rod and up to two bolas, but I cannot add a third bola.
* Also, not sure just because I do play Ark--are bolas supposed to stack? Because they don't in Atlas, and I can't recall now whether there's durability on them or not. I do appreciate that it seems to pull the next one from your inventory without you having to craft it or add it manually!
* Not sure if this is a bug, but some creatures don't report that they're a Level 2 tame until you try to bola them, and then it says "requires level 2!" whereas some have grey text that outright says they're Level 2. The bulls but not the cows, for instance. (I was very excited to get a pack animal to haul all that stone and wood and metal around, and then...pack mule denied. Figured it probably wouldn't work since it said it wouldn't for the cows, but it was worth a try.)
* Raft crew...is hilarious. XD I don't know if this is a bug or just funny as heck, but before we left the starting island, I'd tamed two monkeys and a chicken. We each had a monkey on our shoulder when we got on the raft, but I took the chicken because why not. The raft listed us as three crew--two officers and no sailors. (I made my friend an admin, so that may be why two officers?) We decided the chicken must've been the second officer, though, and declared her first mate. Is it intentional that un-carried (unridden as well?) tames count as crew? I suppose that's one way of preventing an army of monkeys....
Being able to see precisely what status effect we're under would be kind of nice...I don't know all the icons yet, and your "freezing to death" icon looked more like a silhouette with a blue spider, not a blue snowflake, so I was terribly confused since it came up in the middle of a port town. Was I poisoned? Was there a trap? Tiny invisible death spiders? In the middle of a Freeport town? I was all "What is with this blue hellspider?" "That's a snowflake!" my friend says, as I die of cold in the middle of town. XD
* Maybe make the Freeport towns warmer? XD I mean, if you're in a Freeport, chances are you have no idea what you're doing and you're probably in cloth armor.
* Or maybe make the status icons (optionally?) bigger, with an explanation? I mean, I've got two cats that hate each other, I'm not always looking at the screen when notifications pop up.
* Haven't been able to find it, but maybe it already exists somewhere--if it doesn't, can something be made where you can read the starter info again? I missed about half of it because I was trying to sort out our company, and I probably figured it all out on my own, but someone else is bound to want the same thing. Salt does this nicely with lorebooks that spawn in your inventory, which you can always discard later.
* Speaking of Salt...I hate to compare games, I really do, but one dude and some playdough-quality models honestly did a better job of sailing commands than this game. In Salt, you just stand at the rudder or stand at the wheel and mouse-drag to control your ship. The current system in Atlas is super-clunky, and I definitely see why you need a crew--I would die very quickly in a sea battle if I had to steer the ship and man the guns, and unfortunately my friend gets violently motion-sick from sailing in this game, so she's probably going to be incapacitated for the duration.
* I went and downloaded your map maker from Github, and...well, I figured out how to create a map, and island placement, but there are a ton of server-related variables I can only puzzle out by looking at the two samples, and I'm not honestly certain I'm matching things up properly. Some documentation would be nice for the UE4 challenged when someone gets the time! The starting cell is pretty boring for private play, and the world is going to feel very small very quickly without custom maps.
Anyway, sorry for the wall of text...if you have a bug database somewhere like Planet Explorers did, I'd be happy to enter them all one by one! We really did like what little of the game we managed to play, though it was sort of disappointing to realize the entire cell was going to be Freeport and without a second server, there would've been no ability to level up past 8. (And even with a second server, clearly that was not to be!) And unfortunately I can't attach logs because I completely forgot to download them before trying a reinstall...it was very late/early, and I was very tired by then, since initially Nitrado kept telling me no game existed to reinstall. (Freely admitting I'm just waiting for Host Havoc's Atlas servers to be offered before bailing on Nitrado entirely...pun maybe intended.)
Thanks so much, and good luck!