Did I kill my chili's heat by processing the tomatoes and onions together?
So, first, that chili recipe will always be heavily meat-flavored because it has 3lbs of beef in it; at a glance, that recipe is more than half beef by weight.  So if you want a recipe with a subtler meat flavor, that's probably not the right recipe for you.

There are several possible reasons for it being less spicy than you expected, among which are:


the dried anchos and cascabel you used were old and had lost most of their flavor
heat level in fresh peppers can vary a lot; maybe you got ones that were on the less-hot side for their variety
many fresh peppers vaporize a lot of their capsaicin when fried.  So it's possible that adding just the peppers and garlic to the pan could have burned a bunch off; I've had this happen particularly with habaneros


All of that aside, I wouldn't expect that recipe to be super-spicy, more medium-hot.  So maybe you just have a high pepper tolerance.