Any disadvantages of using background transfer?

Hi,

We have over 100,000 files to transfer using the WebDAV protocol. Our plan is to utilize the background transfer mode, which allows us to add additional folders and files to the queue at any time. However, are there any drawbacks to using background transfer?

No.

Just note that by default overwrite confirmations are disabled for the background transfers.
https://winscp.net/eng/docs/ui_pref_background