Which roads in particular were you looking at? I believe that all standard footpaths I've tagged with bicycle=yes and designation=shared_path are directly connected to a shared path without being interrupted by a road. The bicycle=yes tags all end once they reach a road (which is when the shared path ends under the Vic road rules).
This issue was discussed briefly in the Oceania Discord and I made sure that all footpaths I tagged like this have both the footway=sidewalk and designation=shared_path tags so they could be found and updated if we decided bicycle=yes wasn't the best way to tag them. Perhaps we should bring it up again, and in the mailing list too. Melbourne seems to be littered with improper signage on its shared paths