Honestly, I think even the old Caltrain cars were pretty clean. The only dirty parts were the bathrooms (and honestly, train bathrooms are sort of gross most places). Caltrain has always been sort of luxury, though; the median Caltrain rider has a >100k household income, which come to think of it, might be one of the highest median rider incomes for a public transit system in the world.
I think COVID year stats are always a bit sus. I imagine the people who had the option of working from home tended to be higher income. Outside of medicine jobs, the stay home order mostly exempted lower income jobs (eg grocery stores, mechanics)
