I must sayI thought getting mortgage on freehold flats was no great problem? I own a freehold flat in block of nine, they seem to sell OK fairly regularly, but probably at least at a 10% discount because they are freehold. We can all show a history of sharing repair costs like painting outside, new roofs etc. so maybe that helps.
I cannot see why you shouldn't set up a lease on just one flat, but it would need to be managed by a "management company" who do repairs etc. If it was a tin pot company with no history I would think that might also hinder getting a mortgage?