I understand that might be a problem, but we need to conform to the standards and norms of OpenStreeMap and do things the proper way there and not try to work around it due to a bug or shortcoming of 3rd party software.

Can you let me know what software is causing this problem for you? I've heard of some software not handling multipolygons correctly, but they eventually updated their software to fix that problem. Have you tried updating to the latest version?
I'm not sure what you mean exactly when you say you will make "another fairway" attached to the green. Most of the cases there will just be the single fairway that connects to the green and shares the border nodes. Hopefully that is what you meant.
