Your problem isn't going to be the gate agent, it's going to be the available bin space. If your bag doesn't fit in the sizer, it's not going to fit in the RJ bin at all. If you're in J it can probably fit in the closet, but I don't think all the CRJ900s have one.

If you're in groups 1 or 2, you're not likely to get hassled by the gate agent. In fact if they're having a bad day I think they'd be more likely to just let you board and make life miserable for you and the FAs. If you're boarding with general population, word has likely made it's way back up to the gate that all the bins are full and they'll be gate checking everything that isn't going to fit under the seat, doesn't matter if it fits the sizer or not.