Yeah, this is exactly why I do it the way I do it as well. I find it less "effecty" going all up front, and it makes it sound more like part of the instrument.
There are loads of songs where Adam is playing rhythm, with his volume pedal rolled back, with his delay on. He'll often roll the volume up to create a sort of pre-chorus gain swell, and then on the downbeat he'll kick in one of his Boss loop switcher pedals to take all of his spatial effects off as the big heavy rhythms hit.
He'll kick them back on (sometimes with a flanger too) for leads and single note melodies.
On Facebook there is a group called the Adam Jones Guitar Collectors group. I'm a member, I think
@MirrorProfiles is too. One of their long time members (sadly passed away now) started a PDF called the 'Adam Jones Tone Chasers Handbook' which gets a revision every now and then. There's some nice photos of his board in there.
This is the classic board, but he added some extras since Fear Inoculum:
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Honestly, if you want to nerd out about Joanz Toanz... that Facebook group is THE place to go. They've figured out mostly everything at this point, and I truly don't think Adam Jones's tones are all that mysterious these days.
I did love in the early to mid 2000's when it was though, trying to figure out each intricate part of the rig and how I could apply it to my own.