Trimming the rom changes the crc and we only use the crcs for untouched scene releases.
The ds-scene side of the tool is mainly useful as validation that you have the untouched release listed on the site.

It wont work with trimmed roms for a number of reasons. One being that each software works differently to the next one, so for example 3 different trimming tools could all produce a unique crc where they are all using slightly different methods to trim.

This would be an absolute nightmare to support because each rom on the site would need a bunch of crcs listed in the database. It would have to be like:

Clean
trimmed with ds-scene rom tool
trimmed with tokyotrim
etc etc.

Its unrealistic to support all these combinations in the rom database. The tool was made with clean scene releases in mind and that's what it's best used with. I understand what you are saying but in order to please you, retrohead would have to completely change the way the tool gets it's information from ds-scene.