I'm wondering now, weren't the bases we found so far in Alliance space? I might be misinformed about this. If so, why? If not, then we are good I guess...
Good question.
I don't know if there's a better answer already, but this is what I reckon.
In FFE the Alliance was really newly formed. It was basically an upstart bunch of folks (I think mainly Turner and Argent) who didn't like the Feds or the Empire so they decided to make a government of their own with blackjack and hookers. At the time, that area of space was on/near the Frontier (Hyperdrives were a lot slower back then).
It's possible it's a coincidence that the secret INRA bases are in Alliance territory. I mean, I think they were both just "on the edge of known space" sort of thing - since hyperdrives were slower, a system 15ly away (for example) was literally days away, a system 50ly away was like a month away or something. So, the proximity nowadays
might just be an artefact of expansion over 150 years and the new faster hyperdrives.
However... Maybe not... I don't really know if there's any hard facts on it really?
In Premonition, they mention that Mahon (the Alliance leader) is the only current leader to have records from back then, so it's likely that the current Alliance might have known about INRA when everyone else forgot - it's also possible they always did and maybe a big part of what they have been up to is related to INRA research. I mean this is Tinfoil territory, but it's definitely a possibility. They did set up a semi-secret research base way out in the California Nebula a while back researching "meta-alloys" and other stuff. They're clearly doing
something and that something may relate to INRA secrets they got.
I mean, I find it unlikely that the Alliance spent 50 years in that area of space and didn't survey all the planets already. A bunch of people found that base in like 48 hours or something after guessing roughly where it was...
Although, the Sirius connection is good too, they're a big corporation though and very spread out. I've no clue how to chase that one down.