I haven't done a lot of automatic conversion for the reasons you list. However, I do have some success stories worth mentioning.

1. Lines that go from point a to b without deviation come with higher levels of success. Trunnions and the like are also branches, and subject to errors, especially on bends.
2. Lines where the designer routes from point a to b without going back and making reroutes are also subject to fewer errors.

I once had over 8,000 linear feet of pipe pop up into CAESAR from PCF files without any hiccups, also following what a "reasonable analyst" would model. However, subsequent imports would provide outlandish results.

Not sure this helps, but maybe it'll get you closer to a better workflow.