That's a very good question, and I couldn't find a clear answer in Veracrypt documentation.
So I did the experiment :)
FYI : I did this with Linux and GParted for initial partitioning, and of course Veracrypt for Linux for the next steps. I bet it should work similarly on any OS.
So :
I formatted by USB stick with two primary partitions. My aim is to encrypt the second and smaller one with Veracrypt. I put a dummy file in the bigger partition to later check that it was not deleted. I chose on purpose a file system not managed by Veracrypt, namely XFS :
Then I opened Veracrypt and launched the Volume creation wizard, making sure to create a volume within a partition / drive:
I went for a standard Veracrypt volume (i.e. not a hidden one) on my sdc2 partition (that I selected in the "Select Device" menu), with AES SHA-256 encryption protected by password only (my aim here wasn't to create a strong safe, just to test if initial file system can bother Veracrypt).
At final step, Veracrypt asked for a file system. XFS was of course not suggested. I selected FAT :
After encryption, I could successfully mount the encrypted volume, create a file on it, dismount the volume, re-mount it and retrieve my file. As expected, the file on my other bigger partition wasn't affected.
After that, the OS cannot guess what the partition is:
So, getting back to your question, it seems that the partition file system before encryption doesn't matter, Veracrypt will just re-format it.