https://www.ventoy.net/en/doc_search_path.html
tl;dr: create a .ventoyignore file inside the folder you want Ventoy not to scan.
Alternatively when creating the ventoy installation you can chose to leave X amount of space behind the ventoy partition and then create your own data partition there afterwards. You lose the advantage of “dynamically” sharing the available space between ventoy and your data, but with the seperqte partition you can use whatever filesystem you like for your data, and there is a clear seperation between ventoy and your other data.