Yeah, honestly tracking it along two separate axis, one for fat, one for muscle would be perfectly fine by me, hell you could further simplify it by abstracting muscle out as being dependant on stats instead, strength exists for a reason after all.I think the best you can do to balance excessive complexity (this isn't a diet sim) and making weight & physique have both fluff and crunch behind them is to focus on tracking two factors; fat mass vs lean('muscle') mass. Doesn't have to be perfect, but that lets you have more variety in appearance and gameplay. Suddenly, you can then account for four different extremes; anorexic starvelings, 'skinnyfat' folks bereft of tone, burly historical gladiator-like figures with padding over their muscle and bodybuilder-esque folk that look like they jumped out of an fmg game.
Don't get caught in realism beyond balancing changes in both variables. I've seen folk get lost in trying to simulate every goddamn calorie and element of basal metabolism and it was not worth it, lol.
I just wanted to avoid the horror show of trying to wrangle an actual real life system into representing something it wouldn't really do a good job of showing. Some abstracted and arbitrary values would do just fine.