Well there was a changeover of personnel between the Metacrisis regen and the Matt Smith era. Moffat strikes me as the sort of person more likely to be concerned with adhering to rules set down in some classic Who episode than RTD. RTD might just not have considered that there was any limit on number of regenerations, and therefore that it would leave his successor with any issues to resolve.
Even during Moffat's run there were queries as to how many regens the Doctor had left, and he confirmed that he was holding to The Deadly Assassin (but would find a way round it). So it wasn't like it was set in stone; it was Moffat's decision to make a point of it. Had he just had Smith regenerate without bringing up the limit, some fanboys would doubtless have complained, but the history of Who is so inconsistent that it would have been easily justifiable.
Personally I quite like the regeneration caper in The Time of the Doctor and enjoyed the extravagant send-off for one of my favourite Doctors, so it never really bothered me anyway. In common with a lot of Moffat-era stuff, though, it wasn't the most accessible of plots. I watched it with my parents, who had watched Who of old, but hadn't kept up with the new series except the occasional series finale or Christmas special, and they had absolutely no idea what was going on.
And yes, this is it. As was indeed indicated in Time of the Doctor. He suffered a fatal injury, regenerated, and kept the same body. The metacrisis doctor was a side-effect of siphoning off the excess energy. The Metacrisis Doctor wasn't the eleventh regeneration; rather that was the Tenth Doctor from Journey's End to The End of Time.
The metacrisis Doctor was also a heap of inexplicable BS but that's a different issue. For all people complain about Moffat's deus ex machina resolutions (fairly or not) RTD's ass-pulls were much more egregious.