We cannot provide any support in case some specific are used in combination with AE2.

In all cases we will request that these mods are removed when reporting an issue before we take any action on it.
Also note that it is highly recommended to reproduce any issue in a newly created save as they could have causes data corruption in existing worlds in some cases.

Fabric: Sodium

Sodium does not support Fabric's Rendering API, which is used by AE2 to render it's more advanced blocks.
You can use Indium in addition to Sodium to fix this problem.

We do not support Sodium, Indium or Iris due to them not working in our development environment

Performance enhancing mods

• Optifine (Closed Source)
• Performant (Closed Source)

Hacks (also known as "utility mods")

• Baritone

This is certainly not an extensive list and is missing some entries. Rule of thumb is really no support for any such mods.
The only exception might be for anything which is actually open source and we can fix it without having to make workarounds explicitly supporting these mods.

Anything using mixins or other ways to modify our code at runtime

Should be obvious that we cannot support anything outside our control. Ideally all AE2 issues should be reported to them ruling them out as cause.

• the Wireless Crafting Terminal mod for Forge 1.16 causes crafting jobs to be sent to multiple CPUs at once, even from AE2's own terminals.
• Polymorph's AE2 module causes issues and should be disabled if it crashes, until the author fixes it.

Mods extending internal code of AE2

While we certainly do not want to prevent anyone from extending your internal code, anything outside the API package is certainly not considered stable for these uses cases.
If we have to make a breaking change here and potentially break another mod with it, there most likely will not be a fix on our side to revert it. Of course with the exception of actual bugs being introduced and found by it.