Well first and foremost, you will be able to safely transport a lot of things since they don't really have the best checks at all, you'd have to mess up badly in order for a genned/edited pokemon to be blocked from transferring.
For 1 and 3, some legendaries are shiny-locked depending on the game so if you decide to turn them shiny then they'll be rightfully flagged as illegal by pkhex.
For 2, events should pass just fine, though use the event gallery and don't try to gen them from scratch. Would just have to (optionally) worry about the right date for the event, as some will automatically get today's date instead of the date when they were first distributed.