The first was my 78RS, I swapped out the whole front end, forks and calipers from ATE to Brembo units.
I got the parts cheap from a guy building a cafe bike and so I got all the braces, fork legs, tubes and hardware for a reasonable price.
Yes, there was improvement in braking with the change of just the ATE system to Brembo while still using the under tank master cylinder. So, on that bike the Master cylinder stayed under the tank. That bike got wrecked sad to say.
My current project was a 79RT stripped of the fairing for a naked bike. Again, I have swapped out the ATE system for the Brembo system. The stock under that tank master cylinder is still in use. I am again happy with the results.
Cmparing the braking of my 84RT with the handle bar mounted master cylinder, to the under tank master cylinder with the cable does show a bit more play in the lever before things start working on the under tank mc. 
At this point I am not sure if I am going to go whole hog and swap the master cylinder from under the gas tank on the RT to the handle bar.   I didn’t on the RS and was happy.   I am wearing in new pads and if I do swap things it will most likely be next winter’s project as I have the parts to do so.   I want to ride a bit and see if there is any improvement or maybe I will just live with it.
I love the Brembo brakes and I feel it was worth swapping only because I could do the labor myself and got the replacement parts both times very very cheap.
Labor and parts could drive the cost of doing this into the realm of just getting a newer RS with the better brakes would make more sense.
Just as a note I found this site and these guys seem to get pretty wild
                        
BMW Airhead Big Brake Improvement | R90X Designs | United States
R90X Designs CNC Adapters and accessories to improve the braking and performance of vintage BMW motorcycles like BMW R90/6, R90S, R100, R80, R75, R100/7, /7, R65, R100GS, R80GS, R65GS, better brakes, big brakes, big rotors, radial caliper.
                            
www.r90xdesigns.com
Of course the four pot Brembo brakes are the hot ticket on the new bikes, too bad the prices are so high here I might consider doing a swap. St.