This is a list of issues that, after careful investigation by Iris developers, have been determined to be unfixable on the side of Iris. Please don't open issues regarding them unless you have additional information.
These shaders conflict with shaders provided by Iris shader packs. See the core shaders compatibility document. This will need to be worked around on Botania's side by not using a custom shader, Iris cannot fix this.
Similarly to Botania, ComputerCraft uses custom shader programs for high-performance monitor rendering. Unfortunately, this doesn't work with Iris shader programs.
The CC: Tweaked devs have made the renderer switch to VBO mode with shaders enabled, so there should be no issue.
See: cc-tweaked/cc-restitched#1
Beyond potential issues with shader packs, Colored Lights isn't compatible with Sodium, and Iris requires Sodium, so Colored Lights cannot be used with Iris.
This is a fundamental limitation of how portals are rendered when shaders are enabled. They are composited on to the scene after rendering has completed, meaning that they cannot be rendered behind translucent surfaces like water.
This cannot be fixed by either Immersive Portals or Iris without completely reworking how portal rendering works with shaders.
Tweakeroo's freecam has various issues with Iris. We recommend not using Tweakeroo's freecam feature, and using https://github.com/hashalite/Freecam for freecam instead.