Well, looking at the code, both are WAD from Custom Commander: sieges are set statically at least 14 reinforcement waves and defenders are set to auto-charge after the 6th and get re-set to auto charge every 3 seconds, with no check for the mod options setting or whether the defenders are the player's team. :/
Comparing the code to 2.5, this hasn't changed, so it must just not have been noticed before, or at least not as strange. The forced charge for the defender team, even if player, definitely needs to be adjusted. I'm going to look into if I can't puzzle out why there's a static reinforcement wave setting for sieges, rather than the variable. Since CC defaults the # of waves at 20, and sieges here are set at 14, it might be that it was trying to lessen the length of sieges at one time...I'm not sure what's going on here. Natively, sieges have 7 waves, as opposed to field battles having only 2 or 3.