Creating an entity like an assembler with higher than normal quality does not seem to carry that quality forward into future stages. Instead, the entity reverts to normal quality, and interacting with it in future stages record that a change to the quality occurred.
Reproduction steps:
In stage 1, place uncommon quality assembler
In stage 2, observe assembler has normal quality
Seems to happen with all placeable entities, but not to modules with quality in entities like assemblers or beacons. Thanks for the helpful mod!