Width and the fact that there may be spoke holes aside, what are the differences between the two? my tubeless Pacenti rims have a shoulder which I assume the tyre sits on whereas some of my conventional rims don’t. They tend to have a deeper well as well. Both have hooks which serve the same purpose ( I believe hookless rims exist but lets not go there at the moment).
It strikes me that creating that shoulder on conventional rims with, say, tape would convert conventional rims to tubeless capable.
What am I missing? I am looking to create a spare spare of CX wheels without spending money as they are likely to just sit in the pits.

You’ve pretty much summed it up. Tubeless converter kits exist to bodge a none tubeless rim, it’s more or less an old one-wheel-size-less inner tube cut so it looks like thick rim tape with a valve.