The advice you got from the shop is spot on. Upgrades are crazy expensive compared to buying what you want right out of the gate. What a manufacturer can get a part for is a totally different ball of wax than what you can get it for after market. Hold out for what you really want, even if the waiting sucks. I've counseled many newbie friends who wanted to get the cheapest model around, but a bit more money can make a world of difference.
As for color, I loathed the color of my first bike, but it was the right bike for me. Baby blue and dark metallic blue, yeah. Eventually though, it grew on me, mostly because I loved the bike so much it didn't matter. My next bike was more heinous so I repainted it and finally on bike 3 I got what I wanted.
That said, I've ridden through mud, sand and hell with rim brakes and lived to tell, so if the color does it for you, dooooo it.
I think their suggestion to consider non-WSD bikes is a good one, too. While WSD works for some women, a lot of shops sadly treat it as a one size fits all thing. As a rule, WSD assumes longer legs, shorter torsos/arms. I have a long torso, monkey arms and shorter legs. I quickly found the crankarm length on my first bike wasn't long enough (still don't understand the short crank arm logic), but because of its low bottom bracket height I couldn't go longer without fear of banging every rock in sight. So, find out who does their fits and ask him/her their thoughts.
"True, but if you throw your panties into the middle of the peloton, someone's likely to get hurt."