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.

Fruit interior analogy

(wiki-TODO: Add an illustrative image of cut open browning fruit progress, and mabe a sketch of a crude conceptual sketch of a broken open gem based APM system.)

Just like fruits stay perfectly unoxidized inside (especially while still on the tree)
and only start oxidizing and degrading when cut open, advanced gemstone based nanosystems can do a similar thing.
Keeping all the ebvironmentally sensitive things well sealed inside.

Actually even more than that mesoscale compartmentalization could allow for breakage along intended cleavage planes
not exposing interior that is not stable to the environment.
Perhaps overstretchingly extending on the fruit analogy A bit more:
Like multiple seeds in an apple that themselves feature some sealing again.

Related

• Pure metals and metallic alloys
• Chemical stability
• Passivation (disambiguation)
• Nanoscale surface passivation (old: Surface passivation)
• Macroscale surface passivation
• Passivation layer mineral
• Common critique towards diamondoid atomically precise manufacturing and technology

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• Diffusion