For my maps 1) is enough - and warning not even needed. I think it's hard to find out what the outcome should be.
The case of overlapping ways being part of different route relations on the other hand I've seen quite often - in that case I think it's best to just add all route relations to one way, and remove the other one.
The example you found here - I think is quite possible to solve - both restriction relations are identical - so one way including the restriction relation can be removed, the route relations copied over. If the restriction is having different rules - then however I don't think we can solve it correctly (well an exception is if we have overlapping ways in OSM which are oneway and opposite to each other - this is a rare case where overlapping ways are not to be removed I guess).