Sean,
Absolutely spot on with your comments. It constantly amazes me how many fine old courses are butchered at the whim of the new captain/green convener. Yes, I know these guys give there time freely etc but if these guys ran there business's in the same fashion, ie. ignoring specialist advice, they probably wouldn't even be able to afford to pay there green fees. Anyway, thats my rant for the day.
On your question of whether the R&A pick up the tab for agronomist/architect, I have to confess that I'm not absolutely certain. I am fairly sure that the R&A inspect the courses and then make recommendations to the club. Where changes are then agreed with the club, then I think I'm safe in saying that the R&A pick up the tab.
I think the whole involvement with the R&A naturally encourages the club to use the services of an agronomist/architect where they might not have before. The above doesn't conclusively answer your question but I'll try and find out for sure and get back to you.
Niall