Thank you for your reply.
I now realise that base texts are project-specific and that I have been confused by this.
I transcribe the Pastoral Letters as part of the MOTB Greek Paul Project. If I want to transcribe a page on the INTF (general) site, I get a NA28 base text, but when I want to transcribe the same page on the project site, I get a text I think is Robinson-Pierpont (or some other TR/M-text).
So I don’t think there is a problem after all since the change of base text is not global for the VMR