I think it has to do with the inclusion of clickable cockpits as an option.
If the virtual legs are in the way, there might be some switches you can't operate.
If you can't click on the switches, you'll want to map them to keyboard or HOTAS.
If you map everything to keyboard or HOTAS, you might run out of buttons
Look at Black Shark for example. Every single function has a keyboard shortcut and can be mapped to a joystick button. The reason people use the mouse is not because it's intuitive or realistic. Actually, using keys/buttons is more realistic, as in reality even when driving your car you rarely look at which button to press to turn on the air-conditioning, you remember its position, fumble about a bit maybe and flick the switch.
However, unless we have custom made sim-cockpits or expensive HOTAS sets with good profiling software, we will soon run out of buttons to map. Mapping everything to HOTAS also presents another problem...using the same key for many different things depending on shift toggles and profile changing switches doesn't help muscle memory a lot, in fact someone might be unable to avoid looking at his HOTAS, so that to make sure he has the right profile selected before pushing the button.
That's why the mouse is used increasingly in flight sims as a control input, at least for the non-critical controls and i guess that's why even sims that display a pilot have the option to turn him off, so that you can click what you need to click.