Dood, if your custom muffler burnt out, i would be taking it back to them to fix free of cost. Mufflers for piston motors shouldn't get damaged by a little rich running, thats utterally ridiculous.
Swear im not affiliated, but SMB in Sydney do custom rear cans. I personally know of a few people running them in 500-700hp rotary s which run 10-11:1 all day long... thats rich.
As for your question, you have no way of knowing which (either 2 or 1) muffler will "flow" more, as you don't know the internal construction. Slike saying a house with 4 entries and exits will have... more efficiently heating ability ? ?
If you really want to get the highest flowing legal system, custom is a sure'r bet.
PS: What ever your decision, make sure the place your gonging through guarantees the end result... otherwise instead of a can that blew out... you could end up with a illegally loud system.