I don't particularly love the 2555, but on the other hand I absolutely love the later circuit 2205/2210's and the 2100/2500 Mk III is one of my favorite amp designs. Over on the Marshall forums the 2205/2210/MkIII's get glowing reviews, but the 2555's are a bit more polarizing. If anything, I'd say the Jubilee is one of the Marshalls that is most likely to start a forum "tiffy" because it's so different.
That's not to say I hate the Jubilees, it's a great tool and does a few tones that no other amp does.
You mentioned JCM900 and I have to clarify something. The JCM900 2100/2500 MkIII has clipping diodes (gain sensitivity control) but is otherwise close to a 2203/2204 design, just a few differences in gain staging and power amp. This amp might not be everyone's favorite but it's VERY different from the 4100/4500 Dual Reverb. When people say that they hated the "diode clipping" in their JCM900 Dual Reverb, they usually don't understand what is going on - that amp has only a single tube gain stage and the entire design is based on op-amps. Yes it also has diodes, LED's actually, but just removing them does not make that amp an all-tube monster or anything of the sort. Not trying to trash on Dual Reverbs, it definitely has a unique sound that I like sometimes, but it's a big departure from the traditional Marshall sound because it's also a big departure in design, and reducing those changes to "diodes" is focusing on a relatively small part of it. The last JCM900 variant, SL-X, does not have diodes or opamps.
You do have this mixed up a bit. If you are on the lead channel at all, and you haven't modified the amp, there are 5 diodes in an asymmetric array on the lead channel no matter what. If you have the input gain maxed, the diodes are in full force, nothing you do with the output or lead master affects the amount of diode clipping in the circuit. The input gain can reduce their effect on the tone (less voltage going through them) but obviously gain in general goes down since that includes the tube stages too.
The rhythm clip also is not in the circuit at all when on the lead channel, pulling it has no effect. If it does, you might have a short or some other problem somewhere. I have a recently repaired+healthy 2555X right here and the rhythm clip does not make any audible change when pulling out or in while on the lead channel, even set up the way you described.
Not doubting you on the tone of course, it sounds great at lots of different settings.