There is no such thing as an "implied Drive: portion" within the concept of custom formats, or Windows file paths, as far as I know. You're using a relative format. FileBot does not interpret /Media as <drive>:/Media and if you're using a relative format, then the destination path depends...

Note that I saw a change in behavior with the latest update... not sure if it's the same issue as what the OP is seeing or not but for years now i've had formats that began with "\Media/movies/{plex.name}..." which would resolve to "DRIVE:/media/Movies/..." (this is on a windows ...