Comma question - warning: quite possibly opinion based

Well, don't use a semicolon. A semicolon is to separate two interdependent main clauses, not a subordinate clause from its main clause. Only a comma is appropriate there.

As for the sentence you said you "decided on," I'm not sure that employing syndeton is having the effect you'd hoped. It still took me a minute to work out what that sentence was saying, the same as if you'd just gone ahead and used commas between the list items instead of repeating "or" twice.

Sometimes writing something how we'd say it doesn't come off so well. This is one of those times. When speaking, tone, inflection, and pause would make it clear what you're saying, but we don't have that advantage in writing. That's what punctuation is for: to try and recapture that advantage. However, it's a poor substitute, especially when it comes to commas, which are used for so many things that it often makes it difficult to determine what of those many things a particular comma is being used for, like is the case here.

Unfortunately, as much as I detest it, for I'm a firm believer in writing conveying how people speak as that conveyance is why it was invented and is its core purpose, we must sometimes rephrase in order to make something that the shortcomings of grammar renders incomprehensible or more burdensome to comprehend than anyone wants. This is one of those times.

Were I you, I would either move the subordinate clause to the end of the sentence or make the subordinate clause a main clause by eliminating the subordinating conjunction "although" and instead making the ensuing clause a coordinate clause by introducing it with "but," so my "ideas" would be to write either of the following, instead:

"Cedar mulch, wood chips, or coco coir all do well to help with water retention, although I don't much care for peat."

-or-

"I don't much care for peat, but cedar mulch, wood chips, or coco all do well to help with water retention."

That being said, while I didn't change it above, your use of "or" followed by "all" is incorrect, so you should change it. "All" is something you might use after "and." "And" creates plurality, which "all" points to. "Or" doesn't create plurality, which is why we say things like "Tom or Bob is coming," not "Tom or Bob are coming." It makes no sense to use "all" because "or" is saying one or the other or the other, not "all," so either eliminate "all," which is deadwood anyway, or change the conjunction to "and" and accept that it could be misinterpreted as using them all three simultaneously, like in a mix, because that's what using "all" actually conveys, just like "both" would if it were two things. The word that expresses what you actually appear to mean is "each," so you would perhaps change the sentence to:

"I don't care much for peat, but cedar mulch, wood chips, and coco coir each do well to help with water retention."