Its true it is the norm in most cma. Actually you, imo, should train mostly in shoes that you tend to wear on a regular basis, or shoes that mimic what you normally would wear. Discounting of course abnormal footwear. On the other side, its a good idea to make sure and train bare foot, various terrain etc. Just so that you will be familiar with those conditions.
eDit: most grappling excluded for shoes.
For whoso comes amongst many shall one day find that no one man is by so far the mightiest of all.