Been there, done that.
All colony modules are properly configured and displayed, and match their corresponding racial traits. All proper colony techs are displayed for each type of native (rock, ice, gas) at high tech.
The design I'm trying to implement is an exact copy of a legitimate and legal player design. I've done a number of size tests (ship hull, component, etc) that have had absolutely no effect. The AI will design 500kT+ attack ships, so it's also not a factor of size restrictions in the AI_General file.
And I'm using the quick design test you've suggested. A saved game on turn 1 with AI design minister on.