MDG –
The fact that it doesn’t say that it is permitted to put ink on a wound doesn’t trouble me, because people don’t use ink on a wound, they use ashes. Ein hachi nami, if they would use ink on a wound, ink would also be okay.
Your question of why the poskim don’t express a broader heter on all tattoos that are clearly not idolatrous is certainly a good question. I do not wish to say what you are leaning toward saying – that this case is special for another reason, because that goes against the pashtus of the Shach and the Beis Yosef. I would rather speculate that in their societies they simply had no common example of a tattoo that was clearly and obviously not idolatrous aside for medical cases.
Why then is the case of Efer Mikla mutar if tattoos are prohibited by all?
I would answer: Although we are not matir tattoos that are not idolatrous (either like the chachamim, or according to Rashi even like R’ Shimon), that is only because they are similar. I assume this is an issur d’rabbanan, and we are taking the middle ground between Rashi’s chachamim and the others’ R’ Shimon. In a case that there is no similarity because it is clearly and obviously not idolatrous, there isn’t even an issur d’rabbanan; and that is this case.