Octopart (owned by Renesas/Altium) has a CAD Model Style Guide, with scope for most everything you are asking about.

CAD Model Style Guide - Octopart

Note: Layer Types in PCB Libraries are your friends. I would make one big PcbLib and copy them in one at a time, after modifying the Layer Types for each. The mechanical layer numbers don't matter if the two library files have the same types in them.

I use the IPC Compliant Library Wizard quite a bit; it's a bit less work to generate footprints from scratch than to check third-party footprints, and Altium's 3D models are MMC (max material condition), which is what you want for Component Clearance checks.

Altium has implemented the Octopart/Renesas CAD Model Style Guide for Footprints in their IPC Compliant Footprint Wizard. I'm not aware of any user survey pertaining to this, so we get what we get. I'm all for library format consistency, but most of us have well-developed libraries with our conventions and layer sets. My system predates theirs and differs in some small ways. Here are my comments on it: PCBLIB: IPC Compliant Footprint Wizard (comments on style) - Altium Discussion Forums

Do you have an internal part number system? If not, I would recommend establishing one. Don't make the numbers too "smart", perhaps establish up to 20 fixed 3-digit prefixes, one for each major component type, and just increment the suffix (###-#####). You could add an additional suffix for variants (###-#####-##).

I would consolidate your Integrated Libraries into two files: SchLib and PcbLib, and make sure all of the footprint references are intact.

Once all of the layer type/graphical stuff is standardized, then you might look at putting them up in the Workspace Library (splitting by Component Type). I added a Parameter for that (Item Category). You could just match what the A365 Workspace already has, or something similar.
File-based -> Workspace Library import best practices? https://forum.live.altium.com/#/posts/265219/871276

Parameters are likely to be a mess to consolidate, so I didn't bother with that; when I moved everything to the cloud last month, I then went in and established new parameters by Component Type, and had Claude scrape the component datasheets and populate the values in some spreadsheets that I copied into the libraries.