As part of the paths to access Darkrai and Shaymin, the player is required to save the game in the void, so the same risks associated with the Surf glitch occur here, such as becoming trapped without a method of escape. It is also possible for, in the worst possible circumstance, the game to immediately freeze upon loading the save file, forcing a new game to be started. This can be tested for, however, by opening and closing an option on the menu such as the Bag (usually referred to as a Black Screen of Death test), as the game will freeze upon closing the selected menu option, preventing the save file from being damaged.
Bulbapedia
TL:DR Saving in the void for the glitch can softlock you, as can the game freezing on a new save even. The freezing can be prevented by checking the bag. if the game freezes when you open the bag, it means you would've been softlocked. As long as you follow the right path and make sure to freeze check, you should be ok. I'm pretty sure you can automate tweaking anyways
As for your second question, I cannot find anything saying that overstepping and then going back can screw up the setup, and frankly it'd make no sense to screw it up anyways. You should be fine on that front.
