The bottom is pretty flat. There is a section about midship that has a dent in it. 
 

And yes, it does look like it was built that way. It looks like they installed the transom brace first then forced the transom to fit. The brace is too far back.
 

Is the bottom flat?
Does it look to you like the factory put it together that way?

Here's what I'm working with... Looking straight down, here is the transom from the inside. You may be able to see where the brace is bulging the transom outwards near the bottom of the transom.
 

Here's the bulge from the outside:
 

And here's the bulge from side to side. 



I'm thinking I'm going to install the inside board to keep the top of the transom in shape. Then fit the outer boards individually and not put them together first. 

Hey Trey, i find it best to fit and mount everything first, make any modifications necessary then go ahead with the finish. It helps too to get some sealer inside the bolt holes as well sealing up the raw grain in the holes, cheers bud have fun

I like to get everything drilled and fitted before I do any sealing on the wood.
I prefer to bond the two outsides pieces together but the factory left them in two pieces.
I always try to flatten the transom sheeting as much as posable by blunt force trauma, then relive the face of the board enough to make it all fit tight.  

Ok, let's try this again... I'm back again, again.  And I have questions. Again. 

Should I drill the holes in the transom wood and get everything lined up for mounting before putting the finish on the wood?

Should I join the outer two transom pieces or mount them separately?

The transom has a bulge in it where the transom brace has either pushed through, or the transom was bent around. Should I fit the outer boards to the bulge?
 

That mixture is great for stuff that lives outside for extended periods, like wooden outdoor furniture, as it penetrates really well. I apply it every couple of years on some teak benches and chairs and it works great.

The wooden bits on our boats are typically babied a bit more than that so the stain and spar varnish finish is probably more than sufficient and will ultimately yield a better finish.

Spar varnish is the way to go, so easy.
I am a big fan of this.

I have always used stain followed by multiple coats of spar varnish.

Ok, time to get back in the boat. I've got the transom wood ready enough to look into finishing the wood. I found this mixture online. Any other formulas or recommendations?