I bet using ROT on this will lead to unintended consequences because the original characters won't combine but the replaced ones will.
But anyway ROT is a dumb thing to do anyway so it doesn't have any real-world use.
Almost all combining rules (including skin tone modifiers) require a zero-width joiner character between the person emoji and the modifier emoji. So really it's frowning face + ZWJ + brown texture = brown frowning face. (Although technically I don't think frowning face can be modified.) Also, there are relatively few ZWJ combinations.
Technically, there are some older combination emojis that predate ZWJ, mainly the flags, which are composed of two single-letter emojis, e.g. regional-indicator-U + regional-indicator-S = United States flag. So I guess it might be possible to get a couple of those.
And in any case, I think this page assumes that you're staying within the bounds of the basic multilingual plane (it mentions a self-inverting transform would be ROT32768), which doesn't include emojis or skin tone modifiers.
No, the skin tone modifiers apply directly to eligible person emojis; no ZWJ is involved. (Unless other modifiers that require ZWJ are also present, such as the gender signs.)
ab => frowning face + brown texture = brown frowning face => ab