To get exactly the bike you want is darn near impossible with a brand new OEM bike.
One almost always has to upgrade wheelsets, tires, brake pads, cockpit (to match the rider) and definitely pedals.
Of course, depending on the rider and the bike in question.

It's almost always cheaper to build from scratch.
As mentioned, you might still pay what it would've cost you anyway in the end,
but your particular bike will be built to your spec without needing any further investment.

I priced my bike against a CAAD9-1. My bike will be undeniably better when completed for about the same price.
The only difference will be that the CAAD1 will have "some" Dura Ace 7900 parts while mine is mostly Dura Ace 7800.
Other than that, I'll have a better set of wheels than the CAAD9-1, a much better cockpit and just better everything in general.

Or, you can do like I did. Buy the cheapest model you can so you can ride it as you build it and sell off your OEM parts like I did.
I was going to buy a CAAD9 frameset for about $800. (w/taxes). I got a complete CAAD9-7 ready to roll for $815. (incl. tax).
Sold off the some of the drivetrain and cockpit for about $200. So, my current cost is down to $615. and
I have the frameset plus the wheelset that I'll use for beaters in the winter and still have some parts left over.

Plus, it's fun to really notice the difference of an upgrade once installed.
I appreciate it so much more when I have such a direct comparison.

And it "is" really fun to build up your bike and tweak it to your own taste and to personalize it to your needs.

My next bike will be a custom built machine. I'm planning on a Cannondale SuperSix HiMOD
build or possibly a Trek Madone 6.X build for the winter to keep my cabin fever in check.