Considering that his epilogue message seems to be Hero-Worship of Miyamoto, I somewhat doubt that he would hold a grudge against him.
ALttP/
OOA/
OOS/
LA all made sense to follow more or less consistently. And in that vein of thought it then makes further sense to put the first two games at the end of that Timeline. It explains why the Master Sword (aside from a likely non-canon cameo in
OOA/
OOS) never had reason to be drawn again and was instead replaced by the Magic Sword in
LoZ and
AoL.
Aonuma and Miyamoto had never said that the first few games took place on either the Adult or Child Timeline, never really hinted at it.
If you want to get technical there Was almost another game on the Downfall Timeline, with
FSA, if Aonuma had his way that would have been the Imprisoning War, but Miyamoto clearly said he did not want that, so the idea was dropped.
The closest hint we had received that the first two games *might* have been on the AT was that
AoL's world has a lot of water in it and a fairly large ?ocean? separating Eastern and Western Hyrule. However that wouldn't work anymore with the New Hyrule they set up. I believe that theory was most prevalent during the "Great Deku Tree's Success" theory days, where he hinted that he would raise old Hyrule up from the water over the course of time.