Question:
If enabled, it will disable the this mod's functionality.

MOD:
Factorissimo 3
https://mods.factorio.com/mod/factorissimo-2-notnotmelon

Functionality:
R to toggle port markers (requires ALT-mode)

After reviewing the code, I noticed that the factory-1/2/3 entities from the ​Factorissimo 3​ mod are of type storage-tank.

I have already blacklisted factory-[1-3] as well as factory-connection-indicator-* in my local version; I was just testing some other changes I made before uploading the new release.

I have discovered another compatibility problem with the ​Exotic Space Industries​ mod. The following entities are experiencing animation issues similar to the earlier factory-1/2/3 problem:

ei-deep-mining
ei-advanced-deep-drill
ei-deep-pumpjack

I have discovered another compatibility problem with the ​Exotic Space Industries​ mod. The following entities are experiencing animation issues similar to the earlier factory-1/2/3 problem:

ei-deep-mining
ei-advanced-deep-drill
ei-deep-pumpjack

I couldn't find the ei-deep-mining entity definition, but ei-advanced-deep-drill is a mining drill, which is supposed to be affected by this mod if the "mining drills" option is ticked.
Animation issues coming from this would presumably also happen if you inserted speed modules or used speed beacons.

ei-deep-drill and ei-deep-pumpjack are also mining drills, and are supposed to be affected. If these entities normally wouldn't support being sped up (ie. forbidding speed modules and beacon effects), I might consider adding an option to exclude them from being buffed; otherwise, you can always toggle of mining drill changes globally.

I could also theoretically manually slow down the animations for higher quality entities, so all qualities look the same before speed modules ("not running faster, just moving more material"), but that seems counterintuitive...

The problem I encountered is: After enabling the mining drills option, entities like ei-deep-mining, ei-advanced-deep-drill, and ei-deep-pumpjack would spawn two entities when placed. Additionally, when these entities require fluids, their input/output ports become misaligned after rotation. There are also cases where the entities show "not working" animation prompts despite actually functioning. As you suggested, please add them to the exclusion list.

Strange, the content of my reply is always the same 2 messages every time

Are these composite entities, or is there just an issue of the original entity not being removed? If it's the latter, it should be easy to fix that issue directly...

Factorissimo issue should be fixed in 1.2.3; I didn't yet touch EI, since I haven't checked if blacklisting is actually necessary to prevent the issue you mentioned.

Are these composite entities, or is there just an issue of the original entity not being removed? If it's the latter, it should be easy to fix that issue directly...

After removing the first-layer entity, the second-layer entities unexpectedly revert to their vanilla (unmodified) state.