Ah yes, solving design problems by asking players nicely.
In a traditional MMO like World of Warcraft, it's not like you build a base in the starter zone and leave it there for a week, because imagine how many bases would be stacking up. [But] that's kind of how our game does work because you can end up with a lot of bases.
I'm pretty sure most people dislike destroying their own stuff or alternatively, cleaning up. If you're gonna let them have multiple bases instead of just one, what do you expect?
Just speculating but: it sounds like they only tested this with small groups, and that worked. If that's what you're going for, you have to set up the game to play in small groups, not as an MMO... In hindsight they might wish they had put player bases in separate instances.