Does the floor move up and down while you squat? No? Then STFU and train.
No Bullshit: I know a couple dozen guys that routinely squat in the high-300s to low-400s on an aircraft carrier while underway (at sea) and one guy that routinely hits 500+. Also, a few ladies squatting in mid-to-high 200s. You'll be fine.
Judging from the responses, I have momentarily focused on the wrong thing. There wont be an exodus from this recreation centre since I've only observed one other person squatting as you have defined. I will carry on and avoid the rack where I sometimes catch my heel on walk out.
Is it optimal? Probably not. Is it impossible to deal with? Definitely not. These Olympic caliber athletes from impoverished parts of Africa have figured it out. Good luck, man.
Maybe this is a better question to clear up my confusion. If we are so concerned to shim a leg discrepancy of a few millimeters then why are we not so concerned about a similar discrepancy with the surface we train on?
There are so many discrepancies everywhere, best to accept them and move on unless it is enough to impact you. With this being a floor I think you are pretty limited with what you can do unless you go elsewhere.
A little chaos is good for you, overhead press; your wife wants you to put up box of junk up on a shelf, chances are that box isn't evenly weighted. Deadlift; you have a wood fireplace and go logging with a buddy, that thick piece of tree you pick up is going to be awkward too.
I wouldn't sweat the floor too much, your hips may not be level, you may hold one shoulder slightly higher than the other. Measure your calves. You'll see discrepancies all over, fix what you deem important, ignore the rest. It'll drive you crazy.