I have a Builder I've been running in quarry mode (Shape Card (Clearing Quarry)). When it runs (2520RF/t), server CPU jumps from ~13% to ~75%. After turning off the builder, it takes a while (up to ~60s) for CPU to fall to normal levels.

Minecraft 1.12.2
All The Mods 3 4.0
RFTools 1.12-7.00alpha1

Well that's hardly surprising is it? It does a lot of work. A Builder is bound to cause a lot of calculations. This will be the same for any other quarry. But the Builder is very fast so it causing a bit more work.

I switched to a clearing silk quarry and it performs worse (~80%) despite seemingly needing less computing resources to run (not processing drops beyond the original block, not having enough RF to run it at full speed as before).

It doesn't seem reasonable that one block every half second or so is sufficient to account for a 6x increase in CPU use.

Note that you are using an alpha and outdated version of rftools

I'm aware and apologize for that. I'll re-check it once I can get access to the latest version.

I guess something got fixed at some point. I'm unable to reproduce this in 7.12.

I've checked in version 7.01 (though I'm aware 7.12 was uploaded today) and the behavior is the same.