I think there's some bug fixes for 3.1 that weren't in 3.0, there's a piece of paper somewhere that documents these fixes, off the top of my head one is around printing.
The apps that are on the TechIS CD which contains DART versions of LOS 3.1 comes with apps versioned as 3.0 and I don't think I saw them labeled 3.1 - there might be one or two of the apps (well, tools in the right Lisa nomenclature) that are versioned 3.1. But for sure, the USA OS, but not the installer disks say 3.1.
The 7/7 nomenclature does come from bundling the apps. I don't know if the apps were sold separately, possibly with the early releases they were. But 3.1 came as a boxed set complete with spiral bound 7 tool manuals, the Lisa Owner's Guide and a "book" that holds the floppies. Unlike the 1.x and 2.0 3-ring binder ones, these are not modifiable by the end user, I suppose indicating that these are complete/final. You can see the photos in this auction:
https://www.ebay.com/itm/175395193592 for the 3.1 manuals/disks.
There's also a very famous poster with 7 comets that represent the apps, but it shows a Lisa 1... In fact, there's one on ebay right now.
https://www.ebay.com/itm/374250920844 for an arm and a leg. (I do own one one of these.)
The 2.0 and possibly 1.0 ones came with the larger 3 ring binders. If you own these or see the PDFs of them you'll see something strange, example the binder LisaCalc for 2.0 is huge vs the one for 3.1, no idea what was removed or shrunk down, but you could sit and read through the PDFs and see for yourself. You can see an example of the 2.0 binders in this auction:
https://www.ebay.com/itm/175393049907One of the interesting things about the 2.0 binders is that peripherals such as the ImageWriter, 2 Port Parallel Card, the DaisyWheel printer, and ProFile drive came with pages that you would then insert into the 3 ring binder - likely the Owner's Guide. Some of the update sheets would also fit there, though some came stapled (at least the ones I have, some are stapled, not sure if by the previous owner vs Apple Computer Inc.)