I have not yet modded my NTSC-J MD2, so I wanted to try to run this but, I can play only japanese version or unlocked NA version with GG code (removes region lock, CTBT-AA4L AAGT-AN4T RYCT-A6X4). Can either of those two options would be fine for speedruning?

IMO they should be split into different categories. Also not sure about the logistics of that. The J version is slightly different, one of my friends got a copy recently and will be showcasing differerences mysefl in a submission video of sorts.