Is There A Reason for Mono Amps for Ultra-low Noise Class D Modules?

It is likely for practical reasons - easier to place, more heatsink area, easier to repair/troubleshoot, shorter speaker cables, etc.

It's hard for me to imagine that two boxes of the same size would be easier to place than one box in a room. The advantage of greater heatsink area seems lower in the case of Class D amps. As for repair, isn't it more likely that a mechanical problem will arise with two separate mono amps, with separate power supplies, than a single stereo amp? 

It’s hard for me to imagine that two boxes of the same size would be easier to place than one box in a room.

It will be, especially for the large units. You can always shove them together if you want to have single unit.

The advantage of greater heatsink area seems lower in the case of Class D amps.

It depends on the size of class D amp. Some of them, like Rowland 925 have big heatsinks. For the small ones - I agree.

As for repair, isn’t it more likely that a mechanical problem will arise with two separate mono amps, with separate power supplies, than a single stereo amp?

Not really. It is easier to understand what happens without influence of another channel (thru common supply), especially during fault condition.

In addition switching spikes of class D output Mosfets, that are filtered out by Zobel network, can easily get to other channel thru power supply. Electrolytic caps are too inductive to fully stop that.
Audio crosstalk between channels is much less important than this - when one channel pollutes another with high frequency noise. Being in the same case makes it worse because fast transitions will couple to any inductance in the circuit - even the smallest loop.
I had stereo class D amp, that had two separate pockets for each channel amplifier and separate power supply, milled out of aluminum billet. That is not much different than two monoblocks.

Music emerges from the power supplies.
If you have two you have true stereo. They can be in the same box.