Yes, a 2-HDMI output AVR would have the same limitations since there is only one video stream at a time on an HDMI cable. You can't really get around it.
You can bypass the limitation with some of the matrix splitters that can modify the EDID. However, that still means one or the other TV will not get a valid picture (the non-3D will get a 3D picture and not know what to do with it). However, that is an option.
What a 2-HDMI output receiver buys you is less complexity in the handshake which should mean less time. But, there is variability in the capabilities of different HDMI chipsets and how handshaking is done. So, there is no way to guarantee that one set of equipment will have faster handshaking without trying it first.