I think a very simple solution with long term playability is simple. The old claim system for on land claiming and the circle. Change the circle to a hexagon then allow only one flag per person, period. You want more land, grow your company and "attach" the flags to each other. You want to move to a different island...unclaim your flag and move. This would allow for long time players to establish themselves a base, build it, or move it if they want to relocate. As you can only have 1 flag per player, you wont have a shortage of land unless the game actually has the 40,000 players or more it's dreaming of. This claim system works for both PvE and PvP.
Personally, I'd say one server with the ability to flag PvP or not, but if you do the PvP flag is active for 48 hours real time. So PvErs cant jump into a zerg fest and mouth off, if they do they either pvp for 48 hours or stay off the game.
Island claiming by one person, dumb idea. Island slowly getting claimed by a Company through connecting flags, much better idea. If they want to implement island claiming permanently, then allow a Company to only be able to claim one island, can still build wherever but your buildings can be destroyed by other players if you've used your claim flag.
This game is obviously aimed primarily at PvP. But if you try to make it pure PvP then it wont last. PvE content is the long term playability, PvP is typically short term. As fun as PvP is, it does get old after a while and you always end up doing PvE content. The best games that lasted the longest were and are PvE so to dismiss PvE is pretty much a terminal game.
Also, losing everything everytime you die: Initially and for a while it's fun. But after a while you're going to see players just give up and leave because they'll get tired of having to start from scratch. Maybe consider a debuff system with a timer instead of losing everything? Just a thought.
Everyone needs to understand a simple fact in online gaming: there's more PvErs than PvPrs, but theres a ton more PvPvErs that both by themselves combined. You want to create a game to dominate and lead the industry like WoW did? Simple...provide PvPvErs with a game they want to play.