Couple of things:

As long as the WCH(R/S/C) code gets passed along the PNR, you should be good to go. No, a Dr. certificate does not need to be presented.

The "if they can get in the aircraft" question is to see if they can walk the 50 feet inside the aircraft or they will need the use of an aisle chair from end of the jetbridge to their seat. If they can walk from inside the aircraft to the outside, then you can answer No.

Just have them remind the agent in BOM if they need it there. There are plenty of pax that fly through my podunk little airport that don't want it locally but only when they get into the hubs.