Anybody know if it’s possible to apply a custom segment on sales transaction lines to the shipping charges applied on cash sale/invoice (ie UPS/Fedex shipping items)? Standard segments (Dept/Class) seem to apply correctly for the shipping line but not custom segments. Am I missing something?

I don't see anywhere in Custom Segment setup where you can apply to shipping items. You're likely not missing anything. There are still some gaps with custom segments compared to regular ones. Looks like this might be one. You could in theory do that GL line scripting to record it to the custom segment, but that might be overkill.

Huh. Turns out I just needed to apply the custom segment to transaction header as well as line, and now it applies to the shipping line AND the tax line!