I think that there are bigger differences between some 4-3 defenses than there are between some 3-4 vs 4-3 defenses.
Mike Zimmer's 4-3 is significantly different than the 4-3 that the late Jim Johnson used with the Eagles.
Here is a blurb from Bob Sturm:
"Some will say that the Cowboys just wanted to move to the 4-3. And maybe that is all it is. But, if you read this column, you know that I have been saying they have been running a modified 4-3 for Ryan's entire run here. At least half of the game every week is either in an actual 4-3 (nickel defense on 3rd Downs and other passing scenarios) or a modified 3-4 where Ware rushes 88% of the time getting him defined as a DE in a 4-3 defense and the front 3 is just a DE and 2 DTs."