I spent 40 years teaching kids, many of whom had comprehension difficulties, I never came across a problem like you.
There are two separate issues which you seem to have difficulty getting your head round. Your licence for being legally on the canal and your agreement with wherever you keep your boat.
If every time you had used your boat you had it craned out (or for that matter slipped) you wouldn't need a licence once off the water. However the CRT could if they so wished make an agreement with the crane firm that they wouldn't crane in an unlicensed boat.
The situation is similar with marinas. As you know for the vast majority of marinas to be allowed to have access to the canal, agree to various T&Cs. One is that they will not allow boats to moor if not licenced. In turn the Marina makes an agreement with the moorers that they aren't allowed to moor if not licenced. Nothing to do with you and your agreement with CRT it is to do with you agreement with the marina.