It does matter because if you run the JP game with a non-JP region Wii you'll get garbled text for the classic controller warning. This garbled text prevents some SRM from working and also loses a few milliseconds on each reset.

Also for PAL Wii, region-free is not enough, you need to change the video mode as well (you can do it via WiiModLite), otherwise you'll stay at 50Hz, even though you're running an NTSC game.

I'd suggest just using the Japanese preset on WiiModLite to change everything in one go, both for points 1 and 2. You can ignore the brick warning, it only really matters if you use the Korean preset.

Only downside is that you won't be able to access your Wii settings while the console is preset to another region, but you can switch it back to your original region temporarily if you need to change some settings and then go back to Japanese.

Using any mechanic (intended or not) in a dysfunctional manner, dysfunctional in a code sense, i.e. interrupting a state your character should be locked in, going through a collision that should clearly stop you, etc. Cleverly exploiting mechanics in a way that was unintended isn't necessarily a glitch, as long as you stay in the boundary of how the code should run regarding the game state, your character states/hitboxes, and the environment state/hitboxes.