There’s also some precedent in how the French-speaking communities have adopted country subkeys to classify schools, in essentially the same situation that this community finds itself. school:FR has had tens of thousands of uses for the last decade, but school:CD etc. are relatively new, so you may still have an opportunity to convince them that there’s a problem.
Personally, I would be tempted to use those same country codes as value namespaces instead of subkeys, similar to the type:maxspeed or zone:maxspeed values. Country- or region-specific school=* values wouldn’t cause any immediate problems, since no data consumer depends on this key (other than some MapComplete themes). In the future, a data consumer that needs to compare equivalent schools across countries can simply associate school=DE:* values with the correct ISCED levels. But so far, only one Realschule has been tagged in this manner.