Hi,
Question 1)
No. That’s not how Cryptomator works. With cryptomator you create vaults, that are designed for using them with an online provider. Of course you can use them only local, but I think there are more suitable apps for this purpose, like Veracrypt. However: If you want to encrypt something with Cryptomator, you’ll have to create a vault and then put the files in it. Cryptomator will not encrypt existing files (in the context of a of subsequent encryption of your lokal existing files). For this purposes: Veracrypt
Question 2)
this might interest you
https://community.cryptomator.org/t/cannot-access-cryptomator-mounted-drive-as-real-drive