It does look like I got a bit confused there.
The run once per recipe is only the first time the recipe is crafted. Line 4011 of the CS_Core plugin is the line where it disables the run once functionality, so if you comment out that line it'd run every time for all crafts, though.
$gameParty._craftingRunOnce[Ramza.CSParams.resultItem.indexOf(result[1])] = true
I had confused it with the level up common event, which can call a common event, but also runs a block of code before it calls the common event as well. It only happens on level up of the crafting type you're doing though. Modifying the line I mentioned above is probably your best bet.