At risk of repeating myself, and others...
The problem you are having is because the etch is accelerated by the galvanic action of the Gold/Copper galvanic cell that forms, and jacks the etch speed WAY up...
This does not happen nearly as much with Tin/Copper because they are similar in electronegativity (a chemists way of saying they both give up their electrons with a similar voltage applied) ....and also because the Tin forms a nicely non-conductive oxide on the surface, which is a blanket to the electron exchange.
ONLY way to deal with this is to cut exposure time in the ammoniacal etcher.
And this is difficult to predict/preset, as the etch speed of ammonia etchants can vary a whole lot, because the etch ingredients and parameters are mostly uncontrolled, except of course for the metal content. This etchant makes me crazy, and I predict the industry will see a day when both pH control, and air control (via ORP) will be the norm.
Rudy Sedlak
RD Chemical Company