The idea is to raise the level cap of pets' abilities too, not just make them level to level 46.
Mythic and arcane pets should also learn new passive ability at lvl45, other pets at say level 20.

I think this shouldn't be a big problem, just bump their passive ability a bit.
E.g. Kelvin passive ability at lvl15: "A bite attack that damages a target and reduces enemy damage by 10% for 4 seconds". At lvl20 could be "A bite attack that damages a target and reduces enemy damage by 15% for 4 seconds".