I'd also be interested to hear an official clarification. If it is ruled as a special type of overrun, then clearly it can be combined with charging. If the creature further has the power attack, improved overrun and charge through feats, then it's a no brainer as those allow you to overrun one target while charging another, even if the opponent is up to one size larger than you.
Trample gives the targets the chance to avoid or take AoO, so it isn't equivalent to improved overrun in that regard (which is a prerequisite for charge through, which allows you a free overrun of one target.)
I think the size differential would be my deciding factor in the absence of a ruling. If the squishies are only one size category smaller, they may not stop the overrun but they could be considered difficult terrain, thus negating a charge through without the feat. Anything smaller is not going to slow down a trampling creature.
A creature in the way stops a charge unless you have charge through or they are too small to have any chance of impeding your movement. But the same creature does not stop an overrun or trample at normal speed. For charge through to make any sense, it sounds like without it you have to be charging the target of the overrun to use charge and overrun at the same time. I suppose you could charge and trample the same target if there were no other interposing figures or barriers in the way. But otherwise, the trampling slows you down.