Thanks for the detailed response. Pity about not being able to refer to out of tree files from the library metadata but the link you provided gave me an idea: could Git submodule come to the rescue here?
Could we create a sister repo to our ubxlib repo named ubxlib_arduino or some such, which pulls in ubxlib under src? Can one specify a set of sub-directories of src in the library metadata, or does it always want to eat them all up (because there would be things in there related to other platforms etc. that it should not compile)?