Hi,
I just installed a 3.x CLI app and had many of the same questions you had. I can’t claim to know this is correct but the way I viewed the two process is when you have two different servers serving code. If you had say one server serving the angular front end and another server handing the back-end logic (database, oauth etc).
There is a migration guide - did you see that? https://shopify.dev/apps/tools/cli/migrate
I am guessing you did but wanted to make sure…=
Not sure if that helps but figured I would try 