Hi Ian - thanks for the feedback! We've looked at the tags issue in the past, but there's not a good way to bake them into a QT file such that FCPX will read them.
Clip trimming is high on our todo list for a future update.
You can already run multiple jobs - after starting a batch, just pick another set of settings (or a preset) and hit convert all again. Everything will get enqueued. You can also clear all your files (select all -> delete) and add new files if you want to start another batch with new files.