I've just done test (see attached image) and it seems to work as you would want it to. Independent control of L/R inputs, on two volume faders, but each input appearing "mono'd" onto the main LR master output. I'm using an 8-ch NDI source, but it should work the same with a 2-ch camera input.
I've selected "Separate Mono" channels in the General settings, which has given two faders in the mixer panel (bottom right of the image). In the Channel Matrix I have NDI input channel 1 to Master L and channel 2 to Master R. This gives me control of the Ch1 audio on the left-hand fader in the mixer panel, Ch2 on the right-hand fader. In the example image, you can see that there is a signal on both Ch1/2 inputs (on the "Pre" meters) and that, because only the right-hand fader is up, there is only a signal on the right-hand "Post" (fader) meter. However, on the Main Output meters (top left in the image), that Ch-2 input is appearing on both L/R master outputs (mixed into mono, which is what you wanted).

So in Separate Mono mode the Channel Matrix "Master L/R" settings are for selecting which inputs go to the two L/R faders in the mixer panel, and the outputs from those two faders are always "double mono" onto the L&R Main Outputs. The only caveats are that you can only select odd numbered input channels to the L fader, and even numbered channels to the R fader. So, for example, if the two input channels of interest were Ch1 & Ch3, you could route Ch1 to Master L and it will be controlled by the left-hand fader, but if you route Ch 3 to Master R, it won't be controlled by the right-hand fader. It'll actually be mixed with the Ch1 audio with both controlled by the left-hand fader! Could be a bug, could be a feature :)