Kind of weird.

It can rain in deserts?

Well, I was in creative and turned rain on. And I had some issues, when endermen were spazzing out when I was playing normally, so apparently the rain status can be applied, but there are no particles.

I'm not sure if I want to do a rain check in deserts though, because if it happens to be raining somehow, and the tanks don't fill up, then it's the other way round.

How about first checking if it is raining at all then if you are on a desert?

Yes, thats how it would be done. I mean if some mod allows rain (with particles) in deserts and then it is raining and the tanks wouldn't fill up.

Tanks will now never fill up in deserts (InfinityRaider@3722bd3).