I take it then, that all the common info regarding 'sticking to the manufacturers reccomendations', is definately not written in stone. I assume that most of the manufacturers use the old ' balance it at 25% chord', and it'll fly, scenario??
I gotta suggest that those ideas aren't really "common info". Most experienced modelers aren't going to tell you to that mfg recommendations are written in stone. Most of them have seen how mfg CG recommendations often came from nowhere. Of the ARFs I've assembled this year, just this year, I've yet to see but a couple that had a CG recommendation that gave me the impression the mfg knew squat. It's a puzzle what the mfg's use for their CG "scenario." Sometimes I think they're just trying to always insure their customers start out with a very safe CG. But some locations are so "safe" they degrade the design so badly, that can't be the case. And some aren't safe at all. So who knows.......
But you got it..... don't take the mfg's recommendations as gospel. When it's time to work out the CG, do what you recommended and check what the CG software applications tell you. After you've used them a couple of times, you'll find out which ones are reliable (they're probably all going to be more reliable than the everchanging mix of mfg's) and you'll get a feel which app gives you what you like to fly. BTW, the application
http://www.geistware.com/rcmodeling/cg_super_calc.htm suggests that you input your desired safety margin. After you've flown and adjust the airplane from the flight testing results, go back into that application and figure out what the safety margin is for the flight result's CG location. Then use that for your next airplane before flight testing it. After doing that for a few airplanes, you'll have a good feel for using the app to help you cut down the flight test time to locate the CG. And after all, the way to locate the CG is in the air.