Sad to say, Proton's onion service is for their old version. Proton has recently rolled out a new updated version of their service, and as far as I'm aware they don't offer a Tor onion service for that newer version.
So Proton users who like to connect via Tor onion services have been faced with a choice of either staying on the old version of ProtonMail, or giving up on connecting via a Tor onion service. It definitely leaves the impression that they don't care much about Tor anymore, or that it's at best an afterthought for them.
I tested this, and you're right: Their Tor service runs the (in my opinion nearly as usable) older version.
It's plausible that Proton does not care about their Tor service, but there may be another reason: The new version relies more on Javascript code than their old version, and a Tor user is more likely to browse with scripts disabled than a regular user. Proton may be holding back the rollout of the newer version until they have tested it more without Javascript. This is only a hypothesis, and I came up with it just now; take it for what it is.
Using Tor to access a regular web site, ie: through an exit node, is (nearly) no different than using a proxy. Just assume all exit nodes are "naughty" and do your thing accordingly.