Keith, don't know anything about the current status of GEDCOM stuff, but I'm just about to have a play with writing a wee program to add a WikiTree template to all profiles in a GEDCOM and don't know how seriously to take it.
In other words a standard header and footer of plain WikiTree Edit Text are added to a partilucar field in the GEDCOM file. Don't know if that sort of thing would help.
A fancier preprocessor might strip out unrequired fields that are not required.
I realise this is a separate thing than duplicate profiles, but thought I'd ask.