Some interesting ideas. Altering the timers can have strange effects as we have seen in the past on the PTE. This is partly due to timers not all being independent, but linked in some way. Probably lazy programming originally.
Some of the things you suggest I foresee will be difficult to implement.
You suggestion of all players (I take it you mean not just those killing the fortress) are returned to their start positions will probably be difficult. On a 5000 place world there are 5000 start positions, but by the time the fortress is killed there could be up to 25000 bases or more. Some will be from inactive players (because the definition of inactive by EE/EA is 2yrs of inactivity), but the competing alliances with active members will have 10 or more bases. Even if the number of alliances active is small, around 10, that is 500 players with 10 bases giving 5000 bases just for them. Also, alliances would be spread out as players don't always start in the same sector together (although organised alliances who move from world to world will have their starting sector co-ordinated ), If 'inactive' players is defined in some other way than the 2yrs of not logging on then those players will suddenly get a boost by being closer to the fortress and could progress quicker than those teleported to the edge of the world. I can see how that would be abused by alt accounts or opposing alliances. For example, when the fortress is about to fall place alts in one alliance and don't log on for the X days that is newly defined as inactive for the purpose of the transportation.
Having pointed out some of the problems, I like the idea! There will be solutions to the points above.
Currently base levels are restricted to 65 and forgotten bases don't exceed the level of the Guardian bases of 50 - i think the current max is 47 or 48. The fortress max is 95.
Your suggestion of a 50 level increase each time this feature is called means you get level 63 or 64 bases at the edge of the world, rising to 97/8 in the centre after only the first time, and 113/4 after the second time with 147/8 in the centre. I like the idea of them increasing uniformly (or within a range, randomly - eg between 5 and 15 or 2 and 10) as it is likely to be easier to program and get right! The 50 levels is too much, but some increase would be interesting.