1. When I export a transcript, can I have the designations highlighted instead of bracketed?
Yes. Within the transcript view, in Tools > Export Transcript, select Designations on the General tab, and then go to the Work Product tab to select Highlight Text:
2. I would like to select "Comments" to be included in my transcript export, but for some reason it is grayed out and can't be selected.
The Comments option becomes selectable in the Work Product tab when "On Right" is selected for Details. This is because there isn't enough space in the Footer to include Comments, so "On Right" has to be selected first.