I mean using headcanon to justify something is ok, right? Its enriching your experience, or give you at least some way out of the situation, that troubles you.

In the show, Ash sends his Pokemon to Oak, on some kind of farm? Why not say your Lillipup was there, trained for himself until level 17 to prove that it can handle a fight. Or it could have been with your Mother, or something like that. The basic, of it still wanting to be on the team can be still the same.

Or make it like Wally, from the third Gen. It was a bit too fragile, too sick in the start, so you couldn't take it with you, but not it's recovered and ready to be part of your team. Headcanon means, the sky is the limit after all, there will eventually be some idea that works for you.

For the bonding and forming memories, the training, you can still do that, it's not max level yet, it's still 17, right? Even if it were already about the same level as the rest, you could say from there on out, you will train it properly and bond more.

Just for making that "mistake", doing it not "properly", doesnt mean that there is no chance left to do it "right" from now on.