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Don't you find that he is similar to alolan classmates in this way? If I remember correctly, Lana, Mallow or Sophocles were not liked for such traits as well.

Or he believes more in his Pokemon now and allows them to help.

You skipped scene where Alain's tablet-like device detected rise of energy level which led him to watch battle between Ash's Greninja and Sawyer's Sceptile. Only after that Alain wondered why his Key stone didn't react to Greninja's change. But whole process of gathering energy wasn't revealed...

IIRC bond phenomenon has similar nature to mega evolution and its energy was registered by Alain's device. And Lysandre was interested in this phenomenon as well, possibly seeing it as another way for mega evolution. Also AFAIK there was not excess of energy, since all of it eventually was used...

Team Flare could interrupt final battle only in case if Alain's victory wasn't planned by Lysandre. But gathering energy of mega evolutions was Alain's task and he successfully completed it by defeating all other opponents including Ash.