Hey Gendji!
I apologize in advance as this is likely to not be very helpful in fixing your issue.
Mainly because I do not sync to any virtual devices so I have not used this portion of MusicBee before.
But I wanted to point out something that, at least to me, does not make logical sense.
disc-track# format: 0 |- |00
When using the tag <Disc-Track#> the format above shows the total length with padding. So with two zeros in track format a "1" would convert to "01".
Music\<Album Artist>\<Album>\<Disc-Track#> <Title>
Template shows it is using <Disc-Track#> <Title>
So I am unsure of how you are getting "002-Queen-Bohemian Rhapsody.flac" with the above settings.
I would have thought it would be in the form of the templates/ settings outlined above...
1-02 Bohemian Rhapsody.flac
EG: "002-Queen-Bohemian Rhapsody.flac" is missing disk# with dash, has incorrect track formatting, and is adding in additional dashes and <artist> tag.
To me it appears that the template(s) are not being applied when syncing... perhaps (under Library settings) you have auto-organise media files enabled and under "Organisation..." you are using a different template?
Or perhaps your flac files are not tagged properly. Maybe they are missing the tags for <disk> & <track> and the <title> is "002-Queen-Bohemian Rhapsody"
Yeah yeah... I know organise and organisation are misspelled by US standards. That's the way it is spelled in settings dialog which I think is the preferred spelling in British English.