Is my understanding correct that loan words are usually pronounced according to the donor language? (e.g. "das Handy") I seem to remember V is special somehow too, for historical reasons.

If I am reading Duden right, Version is directly a French loanword:

https://www.duden.de/rechtschreibung/Version

while Variation is "influenced" by French:

https://www.duden.de/rechtschreibung/Variation