So something I've seen a lot of in patches is only surface level conflict resolution. While this is fine for certain mods, in others it leads to incompatibilities down the line.
For an example of this just look at Bugnet, the Bug Branch Starnet patch made a couple months back. While it does a decent job of resolving the direct conflicts between the two mods. It makes no changes to any of the content added by Bug Branch. Things like new buildings, new jobs, new decisions, etc are not touched by Bugnet, and thus use vanilla based AI values. This doesn't make them get used equally to vanilla, they instead get drowned out by the content that IS patched for Starnet. Starnet is not shy about heaping loads of ai_weighting onto certain things to force the AI down certain paths. This makes the AI ignore specifically brand new content mods add in favor of the tweaked vanilla content.
Thats why I patch content that mods themselves add, rather than just resolving file conflicts. File conflicts are easy to fix in Irony (which I highly recommend doing), but it won't help with novel content.

Thank you for attending my Ted Talk I will now go huff my farts until I pass out.