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.

The Limited Power of the Comma

Before a coordinating conjunction joining two independent clauses, a comma only signals the beginning of the second clause. Its presence or absence, however, cannot signal whether a subordinate clause at the end of the sentence is to be distributed across both independent clauses or only one: that’s a question of semantics, not grammar.

Like a pronoun, a modifier following what it is to modify grabs on to the first logically available target and tends to stay there:

I chose a pottery class, but Robert signed up for creative writing because it was the only class without a scheduling conflict.

There is no ambiguity in this sentence despite the position of the subordinate clause modifier. Just as it attaches itself to creative writing and is perfectly happy remaining there, the subordinated clause restricts itself to the second clause 1) because there is no cue to read further to parse the sentence and 2) such a reading is semantically blocked by the verb chose, i.e., between at least two alternatives, while Robert’s crowded schedule only allowed him to register for one class.

Your example sentences, however, have been intentionally constructed to introduce ambiguity by subordinating a statement in the gnomic present (“Exercise is good”) or in the habitual present (“Whenever it rains”), both signalling a motivating truth or condition universal enough to be parsed across both independent clauses. Yet you place both in final position, where the tendency is to restrict their meanings to the second clause only. The presence or absence of a comma cannot resolve the ambiguity because it is a semantic one you’ve built into the sentence in the first place.

Topicalization

Consider these two pairs:

I swim every day because exercise is good.
Because exercise is good, I swim every day.

My friend plays tennis five times a week because exercise is good.
Because exercise is good, my friend plays tennis five times a week.

The inversion in italics gives the cause for the action slightly more topicality than the standard order in roman, which a writer might choose for a smooth transition to the next sentence or merely to vary sentence structure for better style.

If you wish to combine the first of each pair using a coordinating conjunction, however, the topicality becomes far greater because it is a cause common to both. Otherwise, why would you utter the sentence in the first place? The usual way to topicalize the cause is to place it at the beginning, just as one does for each person alone:

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

or keep the standard order for the first clause only and let ellipsis take care of the rest:

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

or in some fashion reinforce the universal truth that exercise is good:

I swim every day, and my friend plays tennis five times a week because, as people always say, exercise is good.

Ambiguity resolved, but commas have little to do with it.

Your second example is similarly resolved by placing the condition first or by maintaining normal word order for the first clause:

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

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

Semantic ambiguity can only be resolved by a semantic solution, perhaps aided by comma placement, but don’t demand that a comma do all the work by itself.