So I did get it working, sort of. It was actually reasonably easy to get an equivalent powershell command working, but then I couldn't get it to work being called directly from foo_run, so I had to create a batch script to call it.
You need to create a batch script somewhere on your pc (just create a text file and rename the extension to bat), and paste in the following code:
@echo off
SET filepath=%~1
SET filename=%~2
powershell -command "(& 'C:\Program Files\_personalInstalls\_portable\encoders\flac\metaflac.exe' --show-tag CUESHEET --no-utf8-convert '%filepath%\%filename%.flac' | ? {$_.trim() -ne '' }).replace('cuesheet=', '').replace('CDImage.wav', '%filename%.flac') | Set-Content '%filepath%\%filename%.cue'"
Making sure the path to metaflac is correct. If you don't have it installed it comes from the official FLAC download here.
Then all you need to do is to configure foo_run with:
"C:\Windows\sysnative\cmd.exe" /c "D:\MUSIC.conversion\FLAC\exportCUESheet.bat "$directory_path(%path%)" "$filename(%path%)""
Make sure you replace "D:\MUSIC.conversion\FLAC\exportCUESheet.bat" with wherever you've created your batch file.
The first [ "$directory_path(%path%)" ] and second [ "$filename(%path%)" ] parameters represent the path and file name (excluding extension) to the single flac file that's been created.
The parameters I've included above will work if you've opened the large single flac file in foobar, right clicked and chosen Run Services > (your label). If you want to run this straight after you've performed the conversion (when it's still one file per track in foobar), then you'll need to modify these to whatever you've configured as part of the Conversion destination.
Hope that makes sense?