Oxidation
A common concern regarding the feasibility of gem based APM is that nanoscale parts will oxidize.
(See: Common critique towards diamondoid atomically precise manufacturing and technology)
This is a non-issue though as the (surface facing) target materials are
either oxidation resistant or already fully oxidized.
See: Gemstone-like compound
Pure metals and metallic alloys are not a focus exactly because of their oxidation tendency.
And a few other reasons like diffusion and mechanical inferiority.
See: Pure metals and metallic alloys
Metals still can be mechanosynthesized under certain constraints like
- low temperature and/or
- constrained atom placement freedom
Advanced systems will be able to perfectly seal and safe-keep their internals form oxidation.
To give a weak analogy: Juts like an apples or bananas do not get brown inside so long they're not cut open.