Hum, each subreddit has its own moderators as well. They also have a front page with questions from the different sites[1], though it's not filtered by the ones you have an account on.
You don't need to create accounts with different passwords on SE sites either. In fact, SE has pushed for single sign-on like probably no other large site did.
But you still have to go to a different site to have any hope of getting the chance to ask your question.
It'd be like going to Home Depot and needing information that is related to building supplies but the employees tell you you must go to a different store down the street to even ask your question.
On Reddit you have to post separately on different subreddits, there's no way to simply "post to Reddit" either.
I don't agree with your analogy; I think it's more akin to going to Home Depot to ask for vegetables. I think it makes perfect sense to have a separation between Cooking.SE, Photography.SE, Christianity.SE, etc.
There are a few edge cases, primarily in the tech sites, but I don't think those disprove the model.
Yeah Im speaking primarily about the technical SE's sites. I agree with the completely isolated SE (Photography, Puzzles, religion).
But when you get the related topics servers, programming, security, tools, web development, web apps... All these items are so closely related it's often disadvantageous to try and ask a vertically silo'd question.
I get they are trying to create a detail 'manual' for all questions, but you get to a point where it's just better to read the manual.
[1] http://stackexchange.com/