I see your point. Out of curiosity:
> In a sealed environment in microgravity it's even more dangerous than it is on Earth. / Aerosolized fecal matter can enter the lungs and cause deadly infections.
Would the air filtration / recycling system minimize this risk?
The air filtration will actually help spread aerosols because air currents will carry them through the cabin before they're captured by a filter.
A high power "eliminate aerosols" mode would be one of those infrastructure things that need to be designed (and tested). Even then a single compartment spacecraft like the Orion or Dragon wouldn't have anywhere for the crew to bivouac while some aerosol evacuation mode was active. So you'd want a whole procedure designed around it.
Part of the need for the Apollo Constant Wear Garments was to make up for the lack of faculties in the command module and LEM. Such a thing would be impractical for a long duration mission so toilets (and waste disposal in general) need to be a reliably solved problem.