Is it intentional that runes can be put into assemblers? This would make regular modules completely redundant imo.

No, it isn't intentional. This was a bug in 2.4.0, which was fixed in 2.4.1, so make sure you're using the latest version. If the problem is still showing up, please let me know whether you're using standard or void beacons, and any other relevant mods you're using.

After some investigation it turns out that Null's K2SO Tweaks is the culprit here. After disabling the mod the issue is now gone. Apologies for this false alarm! Might open up an issue on their mod page instead.

Edit: opened an issue as described on their page

Oops it's actually Crushing Industry and not the mod I just mentioned! Sorry about that.

Voidcraft and Crushing Industry are designed to interoperate very well. I guess I'll need more information because I have them both enabled and have no issue with modules at all.

Aaah, the joy of playing heavily modded Factorio. I've done some more intense testing and came to the following conclusions. I have linked my latest log for reference of the mods causing the mentioned issue when present HERE:

• Changing any settings for K2SO or Moshine doesn't resolve the issue
• Changing the void beacon setting of Voidcraft doesn't resolve the issue
• Disabling either K2SO, Crushing Industry or Moshine DOES resolve the issue
• I have tried out the dependencies of those mods in isolation and they do not cause the issue

At this point I don't really know who I should ultimately report this issue to since all mods in combination seem to cause some whacky chain reaction.

Thank you, your testing was helpful. I think the problem is K2's Moshine compatibility code, which is why the two of them create the problem together.

K2 runs its Moshine compatibility code during data-updates. It adds every module category (except two specifically excluded ones) to the allowed_module_categories of a bunch of different entities, as long as they don't have allowed_module_categories defined. This includes the Voidcraft runes. Voidcraft's own code to update categories also runs in data-updates but K2's runs first, so by then allowed_module_categories is already defined. Moshine itself doesn't create a problem because its code runs during data-final-fixes, not data-updates. Now that I know what is going on, I can add code to Voidcraft's data-final-fixes to reverse this.

Anyway, the short answer is, this will be fixed in Voidcraft 2.5.

Heck yeah! I am glad I was able to help. I'll keep the mod config backed up for now in case further questions arise but I am looking forward to the next version of your mod!