My satellite box, dvd and BR players are all hooked up with HDMI and analog connections. Pure Analog (or Pure Direct) does bypass all processing including bass/treble controls and YPAO For 2 channel music, including XM radio off Dish Network, I just prefer analog over hdmi. Give it a try.
Towers might be a bit better in the 80hz - 150hz range, who knows for sure, but you might get better drivers/tweeters in a comparably priced bookshelf. It's a tough call. When using a subwoofer I never felt I was missing anything with a good pair of bookshelves. I wouldn't buy a bookshelf that doesn't go to at least 55hz which would allow an 80hz crossover setting with a little breathing room. But any decent subwoofer wouldn't have any problems with a 120 or even a 150 hz crossover. They're designed to take the strain off the amplifier and the speakers, not the other way around.
Buying speakers on the net without hearing them first is a little un-nerving. But the best place to audition speakers is your own livingroom. I used to rent cars for a few days each before buying the one that I wound up liking the best. Consider the return shipping a rental fee.
Come to grips with the fact that you will never buy the best speakers out there for you. There's just too many different brands and models. Look for an acceptable compromise.