first off, if you are going to remove the Cat, a more methodical approach would be advised. Don't just cut the head pipe, remove, and reweld. Grind the rear weld on the collection chamber off, then remove the Y from the collection chamber axcessing the Cat, remove and reweld at the old weld point. this way it has the appearance of stock, very clean mod.
But the two things we are trying to achieve are reduce heat, increase performance/noise. if we open the muffler, ie, free flow baffles, we get more air out, that in combo with NO CAT gets more air out, but with ramifications. Loss of back pressure, bad low end, but good top end. Seems most of us really want power at the line, and good umph high up. By leaving the cats in you maintain constant back pressure in both cylinders. do a total baffle remove and install a Dummy end cap, giving the appearance of a baffle. All this with a good TUNE, TTS preferably, you will reduce heat, give more rumble; not alot but throaty still. you'll have performance gains through the tune and getting rid of the baffles, like we did long ago. We are concerned with engine/oil temps but there is also concern with exhaust temps. this helps balance the three. For clarification, these are mods that we constantly fine tune and tweak. HD is for ever trying to change it up and so will we. this conversation with Steve was revolving around a 2010 LTD 103, and I had to figure a Big Sucker stage 1 into the mix.
As far as what HD can read, safest bet would be to always load the original ECM settings when going in for major warrantee work. If your going on a long trip, take a copy with you and a small laptop just in case, if you do that HD will not know you where there, no footprint