Surprised that the NR1200 is only a low pass filter for the sub but judging from the manual it looks like you're correct. In a bedroom setting I would not expect the difference to be that pronounced though. You didn't mention the model but Paradigm bookshelves would typically go down to 70Hz or 60Hz. I know my Studio 20v5 go down to 54Hz. If the sub was crossed above that frequency you would get double bass in that range (for example from 60Hz to 80Hz if the sub is crossed at 80). Some people might actually like a little more pronounced bass below 100Hz, but if it's too pronounced, you can dial down the crossover point on the sub until it overlaps with the drop off point of the speakers to flatten the response.
Getting an AVR with bass management would give you a couple things. One obviously is more flexibility as to where the subs and speakers are crossed over. The other might be a little more dynamic range and less distortion from the speakers by filtering out the low bass, but that is more typical for high volumes. If you like it loud and are very particular in your sound, the multi-channel amp allows more control. If your listening is more casual the Marantz should still do nicely.
