[cmake] Only set the native build marker once

Summary: As it turns out, the second time it is set override the cache, which can create strange side effects.

Test Plan:
Modify the cmake module in some trivial way.
Build with ninja, ensure that gen_context is not a problem anymore after regeneration.

Reviewers: #bitcoin_abc, jasonbcox

Reviewed By: #bitcoin_abc, jasonbcox

Differential Revision: https://reviews.bitcoinabc.org/D5020