I'd also love the ability to copy folder structure when transcoding.
For example if I have a song located in
./Artist/Album/Song.flac
and want to transcode it to MP3, my only real option to keep the Artist/Album file structure is to set the destination to "Alongside the originals" and then manually go and delete the originals afterward.
Having an option (maybe a little checkmark box?) to
A: delete the originals (suboptimal option in my opinion)
or
B: copy the file structure from the folder selected after clicking "Import" to whatever you set as the destination would be a very convenient feature that'd save me a lot of time when importing/transcoding songs.

^this functionality can be found in other open source players like foobar so it should be relatively easy to see how it's done I think? I'm not a developer or anything so I'm not sure, just figured I'd mention it in case it helps.