I asked in the GTCE discord about this and it seems to be an Omnifactory issue. You are no longer able to enchant the tools whatsoever.

That being said, you used to be able to do so as is shown in krakaen's Onmifactory LP. (ref: https://youtu.be/unVFVMr51Fs?t=107). I double checked all the change notes to see if there was mention of this being disabled and found nothing.

This is strangely only happening on some of the tools, you can still enchant the hammer, saw, but not the wrench, file, screwdriver, and some other less used tools.

It's possible the functionality was broken after the aforementioned video and has been subsequently fixed in a newer version of GTCE.