This fork uses linked belts to eliminate lag on factory inputs/outputs, which is nice, but it seems that chests are still connected by lua. Why aren't they using the linked chest prototype?

This would have several issues

1. Linked chests void their contents when destroyed.
2. There is no linked chest prototype for logistic chests
3. This would likely cause issues with any other mod that adds linked chests, because Factorissimo would have to override their link ids

Ah alright, that's unfortunate. Thank you for the response, though!

Well, space exploration is another good case of why not. Its control script instantly changes the ID of any linked container placed down to essentially the surface ID of the surface it is placed on. (with exceptions regarding space ship transportation of linked containers.)

Also, space exploration during the data phase actively ties ANY AND ALL research that unlocks a linked container to late game, behind its teleportation tech. (the only override is to depend on space-exploration post process, and define the techs unlocking linked containers in data-final-fixes. Even then, that still doesn't resolve the control issue.)

even if factorissimo were to override a linked containers ID, it would have to do so regularly, as space-exploration regularly resets them back to what it originally set. (every 10 minutes, or when a spaceship launches/docks.)

Also, as for another issue. A chest connection involving linked chests have to ALL be from the exact same prototype, as the chest contents for a given ID are unique per linked chest prototype.

Issue 1 however was valid up until Factorio stable release 1.1.68 (or experimental 1.1.64).

Linked chests void their contents when destroyed.

Thankfully fixed: https://forums.factorio.com/viewtopic.php?f=11&t=103029

This would likely cause issues with any other mod that adds linked chests, because Factorissimo would have to override their link ids

This isn’t true because links only work between chests of the same type.

I’m sure SE shouldn’t be overriding link IDs for all linked chest types so that could probably be changed if requested.

The issue is broader than SE
Nearly every linked-chest implementation I've seen has their own distinct method to handle link ids.

Besides, the current chest connection implementation is already efficient, especially at lower transfer rates. A factory of scale would have much larger UPS bottlenecks.