Welcome to the Cryptomator Community 
from your description i would say this has nothing to do with Cryptomator.
I mean, if your vault is mounted into a folder somewhere on the C:-Volume, of course it looks like the C: is used as a temporary storage, but in fact it is not. Cryptomator en- and decrypts on the fly, i.e. on your real storage device only encrypted data is present and your unlocked vault is just a decrypted view stored in memory.
How do you know that the file is copied first onto your c drive and only in a second step copied to the final destination?