Often the FW (framework) is installed from another party, and that party might be Pega itself, and then the implementation application (you called it "impl application") is built on top of the FW.

If the FW is installed from another party, its rules are likely locked so they can not be modified.  However, if you are the owner of the impl application, you can change your own rules.

Hence I'd expect your first observation that you can't add your impl application rulesets to the fw.

However, I'd expect that if you chain your impl application to the FW, you should be able to see both sets of rulesets when you log in, and then create the application document containing info about both the impl application and the fw.  /Eric