I've read all the various "What is a Hybrid" threads I could find. There seems to be the consensus that a Flat Bar road bike isn't just a standard road bike with flat bars. How is the geometry different from a regular road bike? Can you tweak a standard road bike to fit like a flat bar or is better to just buy the correct frame/bike to start? I've got a group in pieces waiting for a donor frame.

My ultimate goal is something like a flat bar cyclocross rig. I'd like the ability to use large tires should the need arise. Which kind of kills the dual pivot road type frame. Disc brakes are nice but don't really fit into what I want on this project.

A flat bar roadbike is a road bike with a flat bar, there the same thing. The same goes for a CX bike geometry's are the same. If the frame is your size then you can change the stem or slide the seat forward and back.

I would expect a frame designed for drop bars to have a shorter top tube than one designed for flats bar.

Correct.
Why?
Saddle setback (your position sitting on the bike, in relation to the b/b/) and reach to the bars should be adjusted independently. Pushing the saddle back to increase reach on too short a frame upsets pedalling position; adding a ridiculously long stem to increase reach upsets steering.

The best explanation (shortish) I know of is Andy Blance's (Thorn Cycles):

"A bike, designed for drop handlebars, needs a shorter top tube than a bike which is designed for “straight” handlebars. The reason is simple...drop bars have a pronounced forward throw, straight bars have no such throw (they usually sweep back, towards the rider.) When cycling on drop bars, using the brake hood position, the rider’s hands are even further forward. The designer of a well designed drop bar bike, will know that this is where a riders hands are, most of the time and will have taken this into account, by providing a suitably short top tube.

When drop bars are used on a bike which has been correctly designed for straight bars, they will grossly overstretch the rider. I have found that generally, the stem length needs to be reduced by around 60 to 70mm, when moving from straights to drops on the same frame. As most straight bar bikes are designed for use with a stem of from 100 to 120mm, drop bars would generally mean fitting a stem between 30 to 60mm. This is far from ideal.

Conversely, a frame which was fine with drop bars would need a 60-70mm longer stem to achieve a comfortable position
with straight bars. Really long stems, used with straight bars, have a terrible effect upon the steering, making it feel like a tiller! in the position that you have to use, for much of the time, in order to operate the brakes!

I hope that I have been able to explain why we believe that it is so important to choose your bars before you choose your frame.
We also believe that a frame alleged to be suitable for all types of bar, is unlikely to be satisfactory with any type of bar!"

That seems to be the majority opinion. I'm just checking to see if it's better to buy a frame or use an existing one.

Without quoting the whole post, that was excellent. I googled Andy Blance. His site is a wealth of information. That probably explains why MTB's have such long TT's. I'm thinking I might have to go 29er. Though I'd rather have someting a little more road like.

Searching for the same solution. The Surly Ogre is something to look at possibly, or do what you are thinking. The challenge is the added costs and buying a nicely equiped CX bike is pricey and then adding the new components on adds that much more.

I'm thinking about saving my money by buying a Motobocane CX, and then adding the straight bar components : Fantom Cross Pro Sram Rival(this bike is spec'd at about 700 less than anything comprable locally). Adding a flat bar, Sram shifters, a larger cassette, and possibly a Stem should be in the $400 range I think.

Can someone explain what would happen if the stem length is reduced to 30-60 mm? A lot of the conversions reported online do this, and the owners seem quite happy. Why is this trade-off far from ideal?