There are 50000 reels, and digitizing them is not nearly instant - if you just load a new roll each time you pass by the machine, you'll have digitized a tiny random fraction, without any prioritization.
Also it would be necessary to determine if a loaded roll affected by ''vinegar syndrome'' would leave tainting residue in the digitizer, putting all subsequent rolls at risk. That kind of analysis is way above the pay grade of most digitizer technicians, I'd guess.
In practice, the scanner would be cleaned after each roll. This is how we handled motion picture film scanning. With stock in good condition, the cleaning after each reel is not necessary. I can only imagine that a microfilm scanner would by the nature of the format be much much smaller than a 16mm/35mm scanner. To me, that would make the cleaning very tedious and time consuming.
I inherited a box full of microfilm reels from my dad. Some are 35mm and some are 16mm. No sprocket holes, though.
One option is to dither around, and digitize nothing and then it all gets lost.
Another option is to not be a weird know-it-all about all subjects.