I could see this working pretty well, actually. The only problem could be losing it while traveling to where you want to build your base. Because if it registers under your faction name and it is stolen, what would happen then?
As it is right now though, I believe it was just implemented that if your faction buys a second base, your original one disappears. If that is the case, then the devs either don't want us to have multiple bases, or there's another system they have planned and this is just to prevent all the names from being taken immediately.
Either way, I definitely agree with choosing your name beforehand, but maybe with a deposit of 1-2k caps (maybe even higher like 5-10k and that price would be subtracted from the price of the base) to prevent every single person going in and trying to save a name.