JWK/Dunharrow have normal wishing on point. In 2015/2016, a guy in the playgroup I was in decided to abuse the then-muddy wish wording in the rules and interpret it that he could use wishes to pull cards banned in the format. He pieced together a list where the pivotal card was
Time Vault, plus I'm pretty sure that there was a wide selection of silver bullet hosers to go with it. I refused to play against the deck.
That said, learn/lesson does not seem to be anywhere near as egregious. The learn cards are not great, the lesson cards are not great, the pool of available options is quite narrow. I went with option 2 - I'd likely allow this, as if you're rocking a cute STX themed deck then you're probably not going to cause misery. However, I'd prefer not to set precedent and have this remain a thing you can easily rule zero in.
I have no problem with companions - we've already got a commander, what's the problem with shoving an extra card to hang out with them? What does it matter if the formal implementation is sideboard or command zone, the holistic idea still stands, and the construction stipulations are nontrivial. The only companion I've seen in the wild is
Gyruda.
Since we're touching on format rules, I wouldn't mind the 100 card deck size turning into a 100 card minimum instead. If you want to rock a huge singleton
Battle of Wits deck, be my guest. It's a nice callback to kitchen table piles, back in 2005 I was jamming a ~70 card heap of
Plated Slagwurm et al. because I found too many cool cards. No other format has an exact size requirement, and going over 100 is rarely going to be actively beneficial for you. I doubt
Yorion would suddenly become the scourge of the format, but that would be the only thing that would require some amount of monitoring.