I know what you are referring to, I` ve done three BHG`s on three separate Supra`s two before any Supra forums where available. All the heads where skimmed ( shaved ) but I did not seem to have a problem, don’t forget the gasket material is quite thick. I've seen this question mentioned before on other forums and it has been recommended to trim some material off the No 2 timing belt cover if the block has been shaved also. If in doubt I would remove the cover ( you will need to remove the cam gears as you know, not a big problem) bolt down the head and then fit the cover.
By the way I'm properly 5 – 7 hours in front of you in the UK so I can answer you questions before you post them in theory.