What's the evidence that the colors were added later?

[Jorge_Stolfi]

Because these lines were still quite visible at the time of retracer 1, so Rt1 touched up everything else, but left these as they were. Then Rt2 skipped this folio altogether, and when Rt3 got it, only traces left by Rt1 were still visible, but not the original lines, so only Rt1 lines got retraced to their present state.

So you are proposing a variant of the MRT where what I have been calling original (Rt0) is in fact a restoration of an even earlier and fainter stratum (Rt65535).

Pretending that you were serious: the problem with that theory is explaining why Rt0 failed to restore only and precisely those three stars and two arms. 

Seriously, I understand that the MRT is unpleasant because it introduces one unknown variable -- the retracing layer -- for every millimeter of ink trace on the VMS, and thus can explain almost any puzzling detail as a "retracing error".  

But reality is not constrained to be pleasant...

All the best, --stolfi