It was the late pre-season minimum weight change which was specifically said to be to aid the Ducati, despite that bike already being pretty clearly a hopeless case imo, and was dressed up as Honda having cooked a previous vote against a weight change by the manufacturers as being unanimous when it wasn't. Even if there was a previous vote which was falsified (Kropotkin seemed to think this was so) rather than recovered memory by Ducati perhaps under hypnosis, it was held a year after the promulgation of the original regulations under which Honda developed their bike, and was hence an unreasonably late change regardless imo. I have absolutely no doubt the late weight change was precipitated by the dominant early testing form of the unpopular reigning world champion on the original iteration of the 2012 Honda.
The tyre change was actually during the early season in 2012, when Stoner was still looking competitive despite complaining of chatter after the changes to the Honda necessitated by the late increase in minimum weight. The change involved a Dorna-engineered vote by the riders in regard to a choice between tyres, the hard carcass tyre on which Stoner had won most of his races hitherto, and a new tyre; perhaps oddly, the riders other than Pedrosa when given the choice between the tyre Stoner preferred and a different tyre chose the different tyre. Stoner as I recall did not complain about the vote per se, but assessed the new tyre as being likely to prove insufficiently durable under racing conditions, and was proved correct subsequently as even the Tavullia Titan later admitted. HRC were happy for the new tyre to come into use, but saw no reason why the old tyre shouldn't also continue to be available, although I suspect they in reality had little doubt about why that choice was not on offer.