As far as stepping on the plate, like 2019dad said, swing-and-miss is just a strike. Hitter is only called out if he puts the ball in play. As far as interference on a throw, I'll let an umpire chime in on this but I think, generally, there has to be some intent to interfere or movement in a direction that causes interference. If the pitch takes the batter toward the plate, I believe there is some allowance.
I'm hanging my hat on "movement in a direction that causes interference". I'm not talking about a pitch 6 inches off where the batter reaches - and steps on plate. I'm envisioning some pitch over the plate, the kid towing the line, and for some reason stepping out of the box and onto the plate. As a catcher, my first move on some kid leaning in would most likely be to step in front and throw (especially if pitcher is not getting the ball on the inside half). If the hitter does not have sufficient control to stay in the box on a pitch over the plate, that is his problem.
As for having the catcher discuss ahead of time with the umpire, not real sure what he is supposed to say (Hey ump, can you believe this kid?). I would prefer my catcher not discuss potential batter interference or else is might appear pre-planned. Maybe have the catcher step up through the plate on throw backs and demonstrate "interference" during first at bat (step on plate on throw back to pitcher). Make sure the catcher is snug with the plate and not backing up.
On a related note, we have a player on son's team that seems to be getting hit about 1/3 of the time. He doesn't really crowd the plate and doesn't seem to enjoy getting hit. He is on the shorter side and maybe doesn't move too graciously. It almost looks like he's expecting most of the balls to start breaking - they don't and he is not one to jump out of the way). That said, the pitchers are throwing inside on him for no particular reason - I would scout him as getting HBP way too often and work to avoid giving him a free pass (he has zero HR, zero triples and only a couple of doubles so not some huge threat). He seems to have some vacuum effect.