The Patchset is a script that takes the IR3 mod and makes numerous changes to it to effect compatibility with 2.0. A large part of that is a section that runs in data-final-fixes.lua to make corrections to all of the entities, recipes etc. after IR3 is finished declaring them.
The resulting mod from all of this is still called "IndustrialRevolution3", it's not a typo.
One of the things I need to do is assign directions to the pipe_connections on IR3's entities. If Flow Configuration runs data-final-fixes before mine, it will copy a bunch of pipes that don't have directions yet, and the result is that all of your technical "pipe-fc-*" pipes don't connect to any of their neighbours, ever.
At the end of the day, it's technically a bug on my end. But it can't hurt to ask politely. :)