The cobblestone framework generates significant amounts of lag, especially noticeable with more crafter upgrades. I did this as a test:

1. Empty cobbleworks, with auto-output to a chest - barely noticeable lag.
2. Cobbleworks with 1 crafter with auto-output to a chest - brief lag spikes every second or so.
3. Cobbleworks with 2 crafters with auto-output to a chest - persistent significant lag.
4. Cobbleworks with no crafters, connected by a maxed out ExU transfer node to a chest - persistent significant lag.

The FPS returned to normal when the cobbleworks are switched off.
This leads me to conclude that the cobbleworks are causing lag when generating cobblestone, but not when the buffer is full.

Note: I am running Project Ozone 2 which has an insane 30k rf/t power use for the machine, meaning that it might not be noticeable in normal packs. However, it still means that there is space for optimization in the code to reduce the amount of lag.