There should be no issue with warranty. I also lay no claim to be knowledgeable to the extent of the majority on this forum, hence my comment on having sought advice from multiple sources. The Scrambler, in my view, has been produced with many minimal quality stock parts so as to encourage the upgrading of things in particular exhausts and suspension, seats and bars etc so simply changing the end can and removing the cat (not yet mandatory to have one in UK) should be fine. As I suggested, the more you dig for advice here, the more options will be revealed. In my honest opinion, talk to your dealer and get a clear answer as to warranty and as to the viability of a simple switch to the new can. The issues mainly discussed on here about remaps etc are to do with how 'lean' the engine runs, which suggests how hot the engine gets. By not remapping, the suggestion is that there is increased heat in the engine and therefore more wear. I reckon this is debatable. My Ducati dealer in the UK sold me the exhaust and my warranty is unaffected. To follow on, the general consensus on the bikes behaviour with a new can is that the bike is more snatchy but this I have not experienced.
By the way, what was your issue with the Termigioni that the bike has as standard?