You've answered my questions perfectly, and now I feel fully prepared to run the game! The "doesn't make sense" part is what needed to click for me. It doesn't NEED to make sense.
You've also given me the idea to repeat the same real-life song at the beginning of the first few loops, to bake in the repetition even more.
I was hoping to play 2-4 sessions, so that's perfect. I'll definitely let you know how it goes!
I can already tell you though...your module got me more excited for GMing, not just Mothership, but in general, than I've been in two decades. Here's a little backstory...
I just finished running a level 1-10 PF2E campaign, (Gatewalkers) and had requested a break from GMing anything crunchy for 6 months while I rest my brain and prepare for the 11-20 campaign (Fists of the Ruby Phoenix). So for the last couple of months, my friends have been GMing shorter games. We've played some World of Darkness stuff and a GM-less game called The Zone (which was out-of-this-world good).
But after reading your module, I immediately bought several other modules, devoured them, and realized that I'd probably consumed enough content to last our group a year of gaming. So I asked them if I could just GM a giant Mothership campaign, starting with your module...and they said yes! So Pathfinder has to go on the backburner for a while, but oh well. Worth it