You cannot ride any bike with the saddle lower just to avoid the larger drop to your handlebars and/or neck issues. That'll sap your power and probably destroy your knees over the long run.

If you need to raise the saddle to get full extention on your legs (and there is enough seat post to do it), then raise it. The shop can always give you a stem with more rise (a higher angle) to bring the bars up and a bit further back without sacrificing handling. This is, of course, assuming the frame size is right for you to begin with...you can't force a frame to fit if it's totally off.

That said, all of your options sound fine. I also wouldn't worry about taking a bike you bought somewhere else to your local shop just because they wanted you on a Pinarello. If a Pinarello isn't in your budget, then they'll learn to deal with it.

Lastly, yes, there are other bike brands out there that might work. Personally, I rode a Specialized Dolce Comp for a year (Al w/ carbon fork) and found it totally comfortable in terms of frame material (fit was wrong!). I felt a TON of road buzz when I test rode whatever the comperable AL bike from Trek was at the time. It's not all just frame material - it's wheels, tires, air pressure, geometry, etc.... so your best bet is lots of riding before deciding.

And best of luck with the choice! It's great that you have so many options, actually!