The 747 is a eunique aircraft because of it's upper deck. It's not the only aircraft with an upper deck but I believe the only aircraft with an upper deck that can be altered. When Boeing came out with the upper deck for the 747-300, JAL (amongst others) still had some classic 747s on order. JAL asked Boeing to convert these last 2 747-100s to the SUD (stretched upper deck). KLM and AF
also have SUD varients of classic 747s. Boeing also offered a conversion package to extend the upper deck of classic 747s already flying. I believe it is so that any 747 can have it's upper deck stretched or reduced as per the airline's requirements. Hence, any improvements made for the 747-200 could have translated on to 100s that were still being made at the time. Also, new -200s could have been specified with the original lounge upper deck for comonality with -100s already in service.
This is one of the reasons for my love of the 747, it can be customised to suit the airline it works for. There are 747Ds and 747SRs, 747-400Fs with winglets and a short classic upper deck. 747-206B/SUDs with KLM with the body of a -300 and the rest of the plane as a -200. The 747 is the ultimate in modified flying! I doubt there are any two 747s the same between airlines.
I expect even the VC25 could have an SUD if ever needed. The VC
-25 in itself is a customisation of the 747 frame with the original classic body and the newer -400 engines.