You're probably going to see a pattern in my responses ...
1. It's possible you'd damage lighter wheels. My Kona Jake rolls 32h rims with 700X35 tires and I feel a lot less worried about such concerns than if I was commuting on my Trek roadie with 700X23s.
2. A roadie is as "aero" as you make it. Maybe it's just me, but I feel like I'm just as "upright" on my Jake (ostensibly a roadie with slight differences in geometry) than I would be on a hybrid. When I'm out of the drops and resting on the flat/top, I feel like I'm able to be seen very well, and as importantly, to be able to see.
3. No ... in fact, unless it's a "touring" bike or, most of the time these days a "CX" bike like my Jake, you won't find rack mounts on roadies.
4. To my knowledge no. You can get brake levers (interrupters I think they're called?" to put on the flats of the drop bar but they seem unnecessary to me. There's generally enough leverage from the "hoods" and you can adjust your bars/levers til you find your sweet spot. When I'm going downhill fast I'm in the drops, fingers on my levers.
5. Yes ... roadies can have triples. My Jake also has a triple though I don't envision using that small chainring really.
6. Not one brand over the other ... try them all. I own two Treks and now my Kona ... I'm not terribly loyal, especially when it comes to price.
From your questions it seems like you're looking for a touring bike or a cross bike. Either can be changed or adapted to your needs.
The problem is when you say "low-end" .... like anything, you get what you pay for. Low end implies low quality components. If your budget allows, stretch a little and get something with a little better mix of components. Commuting daily or several times a week can take a toll on parts, and it's best to have the best you can afford. They'll generally be more durable.
Hope that helps