So the "endings" are really just variations of the Return to Diadem ending where you refuse to go to the base. They're determined by the amount of probes that you've used (as well as how many humans you slept with), and they only really show an image and give a little post-game blurb about what happens after X2 and Theremin get back.
The option to raid the government base doesn't offer any variations of the ending, it just kind of leaves things open ended for later installments. So probe count, how many humans you've slept with, and failing at the gate won't alter the outcome of that ending at all. Partly because I didn't have time during the Jam, but I also wanted to work on other projects and never got around to adding anything there.
So to summarize; you pick the ending AFTER the second mission when you talk to Threremin and she asks if you would rather Recover the Probes or Return to Diadem XII. The return option has the ending variations where X2's size is determined by how many probes you've used from the earlier missions, as well as how many humans you've slept with. Choosing to raid the base for the damaged probes doesn't offer any different endings.