2. It's been established before that they can hold hands without the block activating
True. Misaki initiated the touch, though. This one is different. Any situation where Hareta starts something with Misaki, that is an action he should only try on a heroine, will usually trigger the blocker. Him pulling Misaki into kissing range should definitely be counted as such, but it worked.
Sure, I'm digging in a bit, but we know bugs exist in this game. Like, the locker incident?
What I suspect is a bug in the scenario (legend about kissing without anyone noticing). One that makes the MC succeed just by bringing a female character to that site - anyone will do, the kiss will be forcefully made to work regardless of affection or any other conditions. Why would that even work with Misaki, you ask? He's male, but the game treats him like a female character in certain situations. Beach event, anyone? Misaki going topless caused censoring - he had to wear a bikini top.
Then there was Misaki's prayer for Hareta's happiness - I don't think that was meaningless.
What I expect to happen is that a set of such events enforce followup conditions in the game that cause conflicting directives and the more those pile up, the higher the chance that the game ultimately crashes or derails completely.