Cheers Winthattt, I've also been doing some googling - some interesting info on Corona Discharge.
I've found two different theories for cause of the brown stuff at the base of the spark plugs, one being the corona discharge as per the NGK article and one being your initial theory of combustion gasses leaking through the plug - NGK seem to strongly discount the combustion gas theory, but either way it seems quite common and 'normal'.
As for my coil boots, the 'damage' that's visible on the outside casing is quite high up and away from the base and sparkplug. I did some more googling on this and an awful lot of my returns are 2zz specific in either the Celica, MR2 or Lotus forums. Whether that's just Google Analytics "knowing me" and being clever, I dunno.
This thread discusses it in quite some detail: https://www.lotustalk.com/forums/f25/coil-pack-arcing-77822/
The state of the coils is described very closely to how mine look: "the small black/brown spots were definitely burn marks and pitting where there had been arcing and intense heat" but this particular forum member was having real running problems with his car, I am not.
As I'm not experiencing any real running problems or EML's I'm not going to rush to swap these, but over winter I'll probably refresh them as part of my annual winter tinkering. I'm guessing that a lot of the posts above involving misfires, idle problems and EML's are people who have had their coils in this state for a long time and the degradation has continued to the point that the spark plug isn't firing properly. I don't think I'm at that point yet, but the burn marks on my coils certainly suggest that energy is "escaping" in the wrong areas, so it's certainly not optimal.