Very odd issue with Ender 3 4.2.7 board

Hey guys, something very odd I found out while installing my blTouch on my Ender 3 last night. No matter what I did, the printer would not respect my NOZZLE_TO_PROBE_OFFSET. I then remembered when I got the board (a few months ago), I had read somewhere on reddit that some boards required x and y stops be reversed, So I swapped them (Initially). This turned out to be an issue for the BL touch, so I had to swap the end stops back, and then swap the STEPPER X and Y. This has fixed the issue with it moving Y when it should be moving X, and so on so forth. I am curious if anyone else has had this odd issue where it seems X and Y need to be swapped on the board? Let me know, thanks!
For the record, I verified wiring, X stop went to X stop on board, Y stop to Y stop. Same for steppers. It seems like something went wrong during the manufacturing of my specific board. Why would I need to swap the end stops for normal printing to work, and why would I need to swap the steppers for BLTouch printing to work?