It's pretty realistic, let it be.
Well, as realistic as something on TPT can be.
You can compress up to 4 element layers per pixel. And energy elements(NEUT ELEC PHOT) can be layered much more.( I don't think infinitely, but alot more than 4)
Element layers?
I actually agree, it broke a lot of saves (Sonic boom guns, anyone?), and what use is it?
It is indeed annoying sometimes. But adds some extra difficulty. It's okay. I once made a weird reactor that worked fairly well, only downside was BHOL clogging up the reactor.
https://powdertoy.co.uk/Discussions/Thread/View.html?Thread=14247&PageNum=0#Message=208716
just look at this discussion
Reasons why this was added in the first place can be found in other old threads, available using the search function. Example
BHOL formation shouldn't really be happening during most normal gameplay (i.e. not involving use of console or PROP tools to put many particles in the same place). Do you still have the save?
Sonic boom guns are possible without layering.