It's not exactly a secret - he was very vocal about his process and there are many interviews and seminars easily available on youtube and such.

There was a few tricks, but no magic at all. You more or less summed it up well.

He believed he should capture band's sound as it is heard by the band itself. On the contrary to most modern music production where each instrument is recorded in isolation, sound is transformed multiple times before it even hits "tape" and in later production you try to recreate a feeling of particular place/equipment/"playing live" synthetically. Which often doesn't work that well - it's like taking bands live energy out of equation to add it back in post processing (good luck).

He despised that approach. Claimed the musician knows how he want's to sound and he is in no position to change that vision. He helped to capture the track more like the musician hears it in the recording/rehearsal/concert room.

He cared about capturing well basic tracks and claimed modern production (mastering) is insanely overhyped and meddles with vision that band had. Which is completely true :)

So in the end he cared a lot about choosing right hardware and microphones (had a collection of several hundreds) while always chose the ones which musician liked. Even if he thought they were terrible in that setting. Because that meant a musician feels that it sounds more to what musician himself hears when he plays. But - the further in the production stages the less he interfered. Instead of messing with ProTools plugins for days, he captured what band found natural and kind of simplified the rest.

He developed plenty of techniques ranging from simple planning (at first step he gave bands a notebook and asked to write down what they want to hear), or not to get underfoot (kept opinions more to himself and chose what musician preferred - which he learned the hard way).

On technical side, he chose to capture more of the room sound of the instruments (especially drums). He also used a lot of microphones placed far in the room to help musicians hear themselves more like they usually hear themselves during practice/concert. For instance, he used sound from such far placed mics into monitors (what musician hears). And delayed them slightly, to give the recording drummer a feeling of actual room size/echo (In spite of his ears being isolated form that). Or did a trick of flipping phase of vocalists microphone when he seemed not confident. In hope to find a setting when bone conduction sound is in phase with headphones sound, so that musician has more natural comfort and simply performs better. Apparently this happened sometimes and I can fully related into "not feeling it" while using studio monitors, despite being few feet from an amp.

Those things indeed make it feel much more like a real band playing next to you. Mostly because the band felt tighter and actually played live together, and not track-by-track.

My favorite recordings of my (amateur) bands were always just single microphone placed in the back of the room, capturing more like it really sounded in there. Very satisfying experience and so different from modern recording and bedroom production.