Heyo, so I'm not sure it's a bug and if so it is a very sneaky one.
But I feel like the alternate recipes cause to have a slightly longer lockout to new materials beeing inserted after the output has been full.
I'm really struggeling to get my full belt outputs, despite overbuilding and oversupply, wich made me use all tools I have to track any detail I could find, and ultimately I ended up just looking at the machine window and observing how uncannily long one single material box was flashing red.

So yeah, I suspect all the recipes from all your mods to do this but I'm most convinced about the science recipes.
I might very vell also have gone totally insane in my eternal war against the UPS but I might also have developed a special sense.
Be my jugde.

On a side note. I'd defiently make yet another base overhaul if you were to just enable the vanilla recipes of nauvis science in non nauvis buildings.

I'm not quite sure what exactly this "longer lockout to new materials" causes, or means for this matter, sorry about that. But just to be sure: you don't mean that the crafting time is too long, do you?
I could easily extend the input and output buffer by a factor, let's say 2 or 4, so that the machine would always have something to work with. Would that help?

About the side note: I could do that as an option for this mod but I tend to make this a separate mod, as this here won't be comatible to overhauls like Krastorio. The new mod, only adding the nauvis science to non-nauvice buildings but the same recipe, then would fit better to K2 and others.

With the Lockout I mean the situation , when a machines output is above a certain threshhold it stops picking up any materials until the output is totally full.
this can lead to one of the supplied ingredients to fully run out from the internal buffer, until the machine is able to output again. Only then will an inserter get active again and provide new material, but my suspicion is that some computation from the mod delays that brief moment until an inserter gets activated again.

I'm not sure if increasing the buffer would help. this unclear threshhold until when a inserter can insert again is the critical part I think.
But I sure would like a bigger buffer, bigger is what i strive for.

Sidenote: I mean I'm all in with your mods and would definetly also apreciate a seperate mod just for more science recipes.