To me the issue is always about rod length vs. cubic inch displacement. Whenever I've gone to a shorter rod in an engine, it is to accomodate a bigger stroke and pick up cubes. Any potential power loss from a shorter rod is more than offset (WAY more) with the added cubes. My 585" SOHC has a horrible rod ratio, with a 6.700" rod and 4.600" stroke, of 1.456:1. And my latest iteration of that engine, which will be 605", is even worse with a 6.625" rod and 4.75" stroke (1.395:1 rod ratio). The 585" engine made just over 1000 HP naturally aspirated, so picking up 20 cubic inches will likely result in an additional 30+ horsepower. No way the reduction in rod ratio is going to offset that.
If you are limited by a displacement rule then fooling around with rod ratios certainly makes some sense. If not, cubic inches always wins over rod ratio. I spoke with a guy about a year ago who went with a 4.125" stroke, instead of a 4.25" stroke, just because of the rod ratio difference. Not the right move, IMO.