I have a bulk compression cell of cobblestone with a decompression module on the network. When there is a spare inventory of cobble (5 blocks), I can pull out as many as I have and it will decompress from the rest automatically. However, if there are 0 blocks and need to manually request an autocraft, it goes back into the ME system and recompresses instantly without the ability to pull any out. How am I supposed to set it up so manual autocrafting doesn't instantly compress?

You aren't. The entire point of that mechanic is so that larger crafting jobs can make use of variants that may not necessary be reported in storage in some intermediate step.

HOWEVER, you yourself as a user are still able to pull as many of whatever variant as you need regardless of how much is reported. Notice what happens if you either shift-click or scroll on a variant even if the system reports none of that variant being present.

Aha! This is exactly what I was looking for, thank you!