I'm not sure you understood what I was asking. Are you experiencing this issue specifically with Extended Vanilla, or just in general? If it does not involve Extended Vanilla, then you probably should have made a separate thread instead of piggybacking from an unrelated thread.
From my testing, I did notice that I forgot to update the basic oil processing recipe so that it could be run in the micro refinery (which is presumably what you are referring to when you say "mini", because as far as I could tell, there was no problem with the mini refinery.
And lastly, this mod does not make any changes to the vanilla oil refinery, only to itself. I was unable to recreate the issue of refinery inputs/outputs being backwards after installing Mini or Micro Machines. Maybe after updating from the previous 3.2.x and 9.2.x versions to the new 3.3.x and 9.3.x, but unfortunately, that's not part of my testing. That being said, the logic for pipe handling should not have changed between versions; I kept that part almost identical