I think the patch panels are stamped slightly larger,so they can be laid over the original floor,overlapping some of the original panel-if you go to butt weld them,then the "ribs" will be a bit too wide and tall,and need massaging,as you said...
I noticed the same thing with rockers--if you chop out all the original rocker,when using the "full" ones,and you butt weld them in.you usually have to take a 2x4 and hammer to the area under the door to allow it to close without dragging...because they are a bit "oversize" and made to slip over the original rusted panel..
I agree proper bracing is important,but often the truck has rusted so badly (on ones I've had up here in salt belt),that there isn't any structure left enough to brace,and your more or less left to "guess" where things used to be,and hope your guess is close enough...