It can work - I ran my Superbe Pro cranks for years on a JIS bottom bracket before I discovered they were actually intended to be ISO.
In some cases it may even be better. Crank tapers enlarge with time as they're repeatedly removed and reinstalled. After many cycles, an ISO axle may bottom out in an ISO crank, and a JIS axle may be a better fit.
But in general it pays to pay attention. A JIS axle in an ISO crank concentrates more stress around the base of the taper, which can lead to cracked or rounded cranks. An ISO axle in a JIS crank may bottom out before the correct press fit is reached, letting the crank squirm on the axle and leading to a mangled interface.
Chainline doesn't have to be spot on for derailleur bikes, but it pays to know what you're doing if you're pushing the limits of derailleur capacity or chainring difference. A more practical concern is having enough clearance between the chainrings and chainstay. Symmetry isn't such a big deal as long as the chainline is in the ballpark, and neither crank is whacking the chainstay.