If you put players like this...
PG trainee - trainee - trainee
SG sg1 - sg2 - none
SF sf1 - sf2 - none
PF pf1 - pf2 - none
C c1 - c2 - none
...and tell your trainer to strictly follow depth chart, I think you won't have problems (unless you're leading around +60 in which case trainer ignores you and puts someone in instead of your trainee - which I witnessed on my trainee twice this season already).
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Normally he wouldn't, but if the coach makes the garbage time substitution when one of his non-trainees is at the line (SG1, PF1, whatever), that player's backup will replace the trainee. The coach will try to put a backup in for every starter, and normally having no backup set for the PG and one for the other positions works, but if the coach can't put PF2 in for PF1 because PF1 is at the free throw line, he's going to just replace someone else.