Robert,
In the moment you would see how useful this is in NUKE, you wonder how one could ever have worked in any other way.
Let me put some light on this. NUKE works with nodes, as XPresso does it. BUT: think of the multilayered file like the facet of the soda fountains, where they have a single pistol like handle on the end. One hose (so it seems) but they press a button and you get a different flavor. Similar to that works the “wire” or “connector” between nodes in NUKE, and it can contain 1023 (1024…) channels in one wire.
So, you connect that wire to a new node, and all the layers of the multi-pass are there at once. You do something with them and create a new channel/layer and feed that as well in it, without perhaps changing even the initial information, perhaps you like to change it and then feed it back into the “pipe” or” wire”.
This keeps the set up relatively clean, and if you ever have had worked with Sony’s (later Apple’s) Shake, you know what I mean by clean, Shake was not, it had 5 channels, not 1023.
If you like to re-render the complete multi-pass, but have already invested a day or two in the compositing, you just reconnect one file instead of, e.g., twenty or thirty! Think of the effort to relink all files with a new multi-pass in After Effects, which is not a nice work. Or re-use one set up for different renderings with the same treatment in the comp-app. NUKE is a few clicks and done, Ae is a mess with large set ups.
On the end you might get the same result, but studios have more interest in fast “turn-a-round” times than cheap apps, hence NUKE sells for a lot of money, Ae does not. Both are great apps and both have advantages, but you asked about the idea to have all in one file [sequence].
All the best
Sassi