I’ve some ideas based on recent work, but I want to make sure I understand your use case: should changes to A and B be independent, but A and B require each other to do useful work?
Mid-reply context preserved below.
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I have a git-inited folder A, called 'Build my web app'. Inside it, it has non-source-code stuff like pictures, pdfs, notes. Also inside it is a folder B, called 'my-web-app-js', which is source code.
[Problem was that making a commit in project B would trigger unexpected changes in A]
Your 'B' use case sounds like one we have right now: A framework, if you will ('A') and apps delivered via that framework ('B', 'C', etc.). Eventually, we will deliver A as a package and the apps as plug-ins to that package (more or less) but right now they all live together (npm run start in A brings in the apps in B, C, etc.).
Our top-level folder has a .gitignore that looks like this:
*
!thisProjectFile.js
!that.css
!images/\*
!otherArtefacts/\*
In A's top-level folder, do a git clone of the repos for B, C, etc., and their folders will be created in that folder, but
1. All git operations in A will ignore B, C, etc., because of the .gitignore, and
2. Operations in B, C, etc., will ignore A, because it is "outside"