Reckon that is a very good Q Glen.
I have three machines including my A with Siamese pipes because I like the access to the primary side (and don't want too many bits - any bits really - to clean). So that's cosmetic, but probably for the wrong reasons!
Two of them have run with twin pipes & silencers as well for long periods, and I haven't really noticed any great difference. Maybe a tiny bit less good at large throttle openings with the siameses - the routing on the A in particular, with a sharp bend inside the downtubes from the left hand exhaust port - could conceivably stifle things a bit I suppose? But then again, those pipes went onto Super Rockets, as you say. (I suppose we should also note that the pipes are slightly different lengths, which some would be 'against'.) Probably have to thrash things to within an inch of their lives to get a true feel for any difference, I think.
Things can sound a bit busier with all the noise coming out of the one hole (hardly surprising) but in terms of normal road-going performance, if there is anything much in it, I haven't discovered it. I've heard it said that Siamese pipes improve the mid-range feel (or even the reality!) but can't say I've noticed that either.
As to silencers/amplifiers I don't know what is correct on anything, but I've run with megas, pattern Goldies (pair and just one) on the A, and standard-type BSA silencer(s) various, and again, apart from the sound I can't tell much difference - except with a megaphone. With that on, this bog-standard siamesed A seems to rev very freely (and frighten the horses), but is less good at the low end. Some of the 'gain' will be an aural illusion though (overgrown teenagers spring to mind); the perceived shortfall may be down to not having done enough tweaking of the carburation to compensate for reduced back pressure.
Whether the picture with a siamesed A is significantly different with higher compression and a lumpier camshaft than mine, maybe others can say. But running the other bikes I have, with compression ratios up to 10:1+ in some past configurations, I can't say there were any obvious differences between separate and siamesed. So I'll be sticking with siamesed when it's a choice.