Atlas is human. The precedent is established by Prairie that Inti will show partially-obscured marks. The gap in Atlas's bangs is too wide to cover the mark completely. Look at her art and try to "draw" a triangle on her in only the space covered by her hair. Doesn't work, the proper position would leave it partially visible, and by quite a large margin.
Aeolus's hair is actually thick enough to believably cover the entire mark.
Note that only the humans that had their bodies fully replaced, are able to be Rockmen. Especially the model A user would require such, transforming the whole body to forms much bigger and much smaller.
That's a baseless assumption. From Albert's perspective, "the mere fusion of man and machine" is a simple matter beneath his evolutionary goals. They require only Albert's DNA; no further restrictions have been specified or hinted.
It is a fact that Model A and A-Trans can handle human DNA, otherwise Ashe's story doesn't work. She inhereted Albert's DNA by birth and her machine body was, by Albert's own words, "completely unaltered." In light of that, one of the following must be true:
A. Ashe's machine body is not a full replacement, or:
B. Human DNA can be mapped and converted for machine purposes.
The only way your statement is justified is if you take answer B and then go on to explain why neither the R.O.C.K. System nor A-Trans can do what Legion's facilities can.
We've seen human bodies transferred as data since the Zero-series, using portable devices no less. There is no reason to assume that technology cannot convert and rearrange the human body two centuries later. I'll also remind you that A-Trans is not bound by the mass of the user (weight mechanics of Bifrost). Assuming for the sake of argument that the human body is incompatible as "raw material" for other forms, storing it as data would be child's play compared to everything else that A-Trans does.