[Big FN Deal]

Granted it's been a long time since I was actually able to utilize the feature in any football game but if I recall correctly, "custom packages" could be achieved with "formation subs" once upon a time. I seem to remember when the formation sub ability, possibly even in Madden, allowed the User to go through every formation and variant, so the User could do exactly what the OP is describing as "custom packages". I think the only limitation was for individual plays but that might have been achievable then too in team management.

I think the specific issue with "custom management" in Madden was with Users using that as a workaround to put any player, anywhere, which becomes an exploit due to the games programming. That said, I don't think it's a big deal to just limit "formation subs"/"custom packages" to the same restrictions as the general depth chart, ie only players from certain "positions" can be interchanged.

Anyway, the general consensus with regard to this stuff is, add it back to team management/pregame, not just the gametime menu/sideline version.