Many questions!
Is it an indie or a chain?
Are you sure it wasn’t mentioned before somewhere?
Who pays full whack for their MOT? There’s always an offer on….the only time to pay full price is if you are worried about getting scammed for repairs in which case take it to the council depot who will MOT but don’t do repairs so have no benefit to making up spurious work.
Company does have a duty of care to its employees, so making sure cars are clean and Covid free could be considered reasonable. How they do that and whether you should pay is another matter (but don’t make this an anti-covid rant, it is still a real thing)
Not wearing masks – maybe their RA considers the risk from employees to be minimised now whereas the wider public may still be less easy to control. Perhaps you could have asked them to if you wanted?