I actually just got done reading Draw Steel!'s advice on encounter building, and I think they summed it up nicely for any D&D style RPG. It read something like (not verbatim):
It's not science. There are too many variables to create encounters using any system design. Too many monsters. Too many variations on character builds. Too much chemistry between character builds. Too many maps that help/hinder. Too many magical items heroes might have gathered. Too much variance on the tactical skills of players. And too many variables in a swingy dice system. Too many variables to ever have an efficient encounter design builder.
To me, that sums it up quite well. I mean, you yourself spotted the inconsistencies at the beginning of your post. So my advice would be to start building encounters that fit your environment, story, PCs, and players. I think you will slowly begin to understand that none of the encounter design stuff matters much. It is mostly about common sense and those variables, and that is what you need to focus on.