I am unsure whether or not this is a bug, but I assume it is. It seems the onCollideWithParticle method is called, not when the two particles are within the same block, but when they are in adjacent blocks. The easiest way, that I have found, to see this is by watching Concentrated Particles being sent up upon creation. The concentrated particles are sometimes sent upwards in one of the adjacent blocks as opposed to the block where the particles' paths will intersect.

Above is an example of what I am referring to. One would expect the concentrated particles to be created and sent up above the lit redstone lamp, but it can be created above any of the 3 redstone lamps in the bottom right. The other redstone lamp is merely to show where the clay and coal particles should intersect to create the split ones, and it is difficult to see that the split particles are also sometimes created above a different, adjacent location.

Again, if this is intended behavior, I apologize for wasting your time. I felt it was important to bring it to your attention, however, if the particles are meant to be created/change above the block where their paths will intersect. This is mostly due to how Forge/Minecraft will handle entity collisions as they only need to touch, so to correct this error, custom code would need to be written to determine whether or not the particles are occupying the same block. In my eyes, this mod has a significant amount of potential, which will be decreased if it takes a wrong turn (I couldn't help myself from making the joke). This mod is going in the right direction by encouraging interaction with blocks in the world as opposed to all particles interacting within a block's GUI. I cannot wait to either find, or possibly create, documentation for the different elements of this mod, and until then, I will be happy to provide more information for you regarding this issue or any others.

I asked jakimfett about the documentation, as I wanted to make it since this mod will be a part of my modpack. He said that I should commit to the wiki of this repo, I guess you can do it too.

By the way, a nice presentation of the problem/bug!

Thank you for the compliment! As for the wiki, I will keep that in mind if I ever find anything interesting to contribute to it. Good luck with the documentation! It is a fun mod to play with in a pack.