If you cheat the hinge up a little on the lower cowl it won't show any of the loops. Mask the loops when you paint and it disappears in the gap. You can buy wider hinge stock from ACS to give you more to play with. One length of hinge will do both sides.
As Ed says above, you can get the two cowl halves pretty close and the hinge segments will basically disappear. However, don't get the cowl edges too close together -- leave sufficient room for slightly rounding the cowlings' sharp edges and add clearance for the thickness of the paint layers. You will (and should) be removing at least the top cowl frequently to check on the engine compartment condition so expect some inevitable wear, scratches, paint scuffing, etc.