I'd argue that weight loss
isn't a confounding variable, as resolving dyslipidemia and MetS is actually one of the main points of the intervention. As for "masking the underlying issue" - let's face it, if you go back to regularly eating a terrible diet, yes, you'll become unhealthy again, but the same would go be true for any chronic insult.
Personally, I'm a believer in metabolic flexibility and I do take time off (vacations, parties and special events, or just when I feel like it) to indulge. The difference now is that I am more acutely paying attention to how the food is making me feel (turns out for example when I have excess bread/sugar, I end up getting a pimple or two that I had originally never connected to being driven by dietary excesses), having a framework to think about how the food will affect my health (what do I think my liver glycogen levels are at?), and much pickier in general about how much I'll eat (my "worth it" taste bar is much higher - if it doesn't taste good I can now just stop). I also feel like I now have effective tools to pull various metabolic levers, whereas before I didn't.
Regarding thyroid numbers, IMO taking about what is "optimal" is actually much trickier than "in range" (which are just standard deviations) because they need to be taken in the context of how you actually feel and if you present any symptoms (for hypothyroidism that would be fatigue, increased sensitivity to cold, weight gain, muscle weakness, etc) - which may be another reason people don't post numbers. Surrogate markers are most useful 1) sequentially per individual and 2) need to be considered with whether those numbers actually correlate with symptoms/reflect pathophysiology. Some are pretty obvious, but thyroid numbers seem to be one of those that requires a lot of careful nuance, but seems not worth the trouble (tracking TSH, T3, T4, rT3, rT4, TPO, Tg) unless you're presenting.
For kidney issues, eGFR is something you'd look at, you'd want to take a look if any of your CMP numbers are out of wack, but I personally wouldn't be worried about acidosis - it's almost never a problem for non T1Ds (would be a sign of a major insulin:glucagon issue at least) but you'd definitely know (and need to know) if it were an issue well outside of regular bloodwork.
If metabolic rate is a concern, I think RMR and DXA are a much better combo for tracking, btw.
As for prolactin, if that's something you want to track and can use as a long term marker that is actionable for you, great, more power to you. It looks like it's only $60 out of pocket, so not terrible, but just recognize that if you throw it out there as something that a number that people should know or care about, or that you want to compare with, it simply won't be.
For chronic stress, I'd suggest 24h cortisol, and maybe some inflammatory markers (I use hsCRP as my one catch all canary, but other common ones include ESR, IL6, TNFa), but for most people, you'd probably get more value day to day from mood and sleep tracking (especially ones that can track HRV or CNS values like the EMFIT).
Calcium is measured via the CMP and deficiencies would I suppose show up in a DXA as well (eg if your bone density Z-score was quite low), but again, I think that's a thing where you'd only be worried about it if you were presenting symptoms (extreme fatigue, hair and nail issues, sleep issues, etc).
I do think that if you are trying to track down nonspecific issues (eg "fatigue") you're going to have to do a bunch of detective work, which may involve more and more esoteric labs, but I'd also posit that most of those could probably also be addressed by relatively simple lifestyle interventions, starting with an appropriate/nutrient-dense diet and the most basic mood/energy tracking (eg:1-5 phone app like MySymptoms or Daylio correlated with interventions), and an engineering mindset.