I've gone through this same workflow and had success all the way through DRC ruleset passing with JLCPCB-based settings, ordering, fab, and use. Board was ordered with PCBA (they did assembly of the stock components) and I did SMD for just the oddball module/ICs they don't stock. Works exactly to design.

My boards are for hobby use and are ridiculously simple though compared to anything professional (breakout boards for specific components in FPV drone video transmission subsystems). That's probably an important detail. I think its like anything else in AI right now. It can do it 90% of the time but that 10% can be really rough and if its a task you can't do or verify yourself, you won't know the difference.