I want my handle bars and saddle to be at the same height on my road bike. I am 51, over weight and not due to sitting so much at work and an old injury not too flexiable. I am not into racing but love the characteristics of a race bike, quick acceleration and handling. This means using a really ugly riser stem or a bike that is a couple of sizes bigger than fashionable, I am ok with the bigger frame. The question I have is will the bigger frame be a poor handling machine?

I wouldn't recommend a "bigger" frame, just one with a taller front end, like many endurance bikes have. But I would do the riser right now because it is a cheap mod that will tell you if your planned position is going to fix your problem. Sometimes sitting up more causes other problems.

Bars and saddle level should be easy to achieve with an endurance frame. Look around, talk to people. That won't be too upright, should be fine. It's the usual long distance setup for many riders, even skinny ones. More important IMO is reach. Sitting on the bike, with forearms horizontal, your elbows should either be in front of your knees or have little overlap with them. For some reason, many people buy frames which are too small.

Because the sales people think we are all pro riders. Or sell what they have in stock

I really don't think it is a conspiracy, just a trend.