Switzerland and the Netherlands have also only one single GTFS feed. So this should not be a problem.
The analysis is broken down into tariff zones but there are pages for complete countries like all railway routes in Germany.
Well the proposal tried to solve the situation for several GTFS feeds and stop ids for one object. It had only a few votes and even the author back-paddled a bit as can be read from [RFC] Feature Proposal - GTFS Tagging standard - #32 by ToniE onward.