Wow, thank you for the detailing all of this!
I do like your proposed solutions for athletics and think they'll be plenty once it becomes another stat improving in the background and not the shiny new toy. If I could be greedy I'd also appreciate it Vega herself got some love in more availability before too long. As someone who did figure out the importance of the extra steps of shower, shake, & spotter, the point in the current system that I felt got frustrating was her sometimes disappearing when the hour rolled over during all the little time jumps involved in getting 100% ready before the workout. More worryingly, it made me feel like spending time talking to this character who I did like was a risk not worth taking if it meant she might leave before getting a set or two in. I think a small system quietly providing a little stability would go a long way in alleviating that particular feeling. I don't know what would feel best and not break the current codebase out of static guaranteed hours 2 or 3 days a week (I hope that's not already a thing and I'm just unobservant/bad at scheduling my gym visits), some logic in the background preventing her from leaving if she and sable are in the forge and the protein shake or showered status effects are above some amount of time left, or something else entirely I couldn't think of. I could also just get over myself and always fully level athletics before getting trying to get to know her, and the moments during the workouts and level-ups are great by the way, but I also want more people to properly appreciate the living bronze sculpture and sometimes plumber even after she becomes non-essential to timely gains.
I'm super torn on voicing support for relaxed/multiple romances. As you mentioned, the story's only just begun. There's a lot of time and potential developments to deepen and complicate relationships. I already love what we've seen from Sable and the multitudes she contains. I love that she can be almost paralyzed by what she has decided are her inadequacies and the legacy she has to live up to and yet not too worried about checking crabholes on the beach after being explicitly warned that the sea tends to eat people after dark. I can absolutely believe that she and we will experience things that leave her ready to make a decision about who she wants to spend her life with.
More importantly, I think you should write what you want first and foremost. Your writing is, in my opinion, far and away the best part of this project and adding material or working under constraints you're personally lukewarm on should be an extremely low priority. Relationship dynamics are hard enough to get right with two people, staying on the pulpy fun side of group relationships seems herculean and hard to justify implementing for a cast not intended for it from the start. I would hate for any reader who has or finds a favorite character to reach the end of her story and come away feeling like it was closer to part of a checklist or a prologue to a poly relationship they don't care for instead of the fairytale romance she deserved.
With all that said, there remains the primordial urge to see Sable doted on. This raises a logistical issue that she has a forehead and two cheeks that all deserve to be kissed while she's told she's doing a great job but most love interests seem to only have one mouth to kiss with. (No spoilers about any eldritch monster romance options, please!) It's not feasible and would almost certainly make for a worse story overall, but the irrational heart still yearns to see everyone get together in all their own unique wedding dresses for one big end card style event and I definitely haven't gone to bed thinking about any multi-party stories like Tavi and Nim working together to build a sybian.