I wasn't being totally serious in my last post. The cameo did indeed happen, but as you pointed out there's more than one explanation for it. Though, there are some things that actually make them being the same universe more possible than they seem at face value. For instance, the Skrulls, Kree, and some other aliens are actually from other galaxies and some combination of SHIELD, Hydra, and other groups could be the origin of Section 31. However, again, as you pointed out, there's still too many differences for them to be the same universe. The most likely possibility is that they're parallel universes which share some elements of history, but also diverge significantly on other important points.