Comma before a coordinating conjunction in compound-complex sentences?

As far as I know, it’s a rule that a comma is needed before a coordinating conjunction that joins two independent clauses. But the use of a comma before a coordinating conjunction that joins two independent clauses in a compound-complex sentence seems to change the meaning of the whole sentence. Please compare the four sentences below.

1. I swim every day and my friend plays tennis five times a week because exercise is good.


2. I swim every day, and my friend plays tennis five times a week because exercise is good.


3. I always feel fresh but John always feels somber whenever it rains.


4. I always feel fresh, but John always feels somber whenever it rains.

I think that in 1. and 3. the context of the subordinate clause applies to both independent clauses, but in 2. and 4. it seems to apply to the independent clause that is adjacent to it.

Therefore, if we want the context of the subordinate clause to apply to both independent clauses, the rule that a comma is to be used before a coordinative conjunction that joins two independent clauses should be exempted in these cases. I have tried to find reliable references that state such exemption, but I rarely found one. The two references that I found (which were from small websites) said that a comma is not needed in such sentences with such context. I cannot find more references to confirm this opinion, so I’d like to ask for more opinions here regarding this.

N.B. I’ve checked the previous posts but couldn’t find the one that exactly addresses this question. The one that I found similar is “Comma before conjunctions in predicates containing two coordinate clauses”. But that one is about comma before conjunctions in predicates not comma before conjunctions that join independent clauses.