Didn't wanna highjack, but I'm just starting a new coop and duck house/hut for our critters that'll be sharing the same orchard run, and your thread struck a common chord so I thought I'd chime in. The Trex won't rot, but the rounded edges and seams might be a PITA to try and get clean. Small gaps are great places for pathogens to take up shop.
I've been all over the place on this one as well. My ducks are gonna get an insulated hut, close to the ground with a screen floor over a plastic tray that I can pull out. We want to put a living/green roof on top of that and on the separate coop, to help mitigate extreme temperatures and provide some more grow space. I haven't completely decided yet, but the walls of both will either be FRP (fiberglass resin panels) glued to cover the plywood walls, or maybe an epoxy coating, or one of the newer super H.D. acrylic coatings (if I can find any info on how peck proof/chicken safe the stuff is). Wifee saw some stuff on the DIY channel that we've played with some called Roll Stone that is incredibly strong, I just need to make sure it is bird safe.
I've read a lot here about people using sheet vinyl flooring to provide a scrubable surface, but I was concerned about sealing the corners in a way that didn't end up being a dirt and germ trap. The FRP is wonderfully tough stuff, but it usually has a textured finish that I'm thinkin' might make pooh scrapin' a little meaner. As strong as it is, it still requires trim pieces and caulk to be watertight, so that all goes back to the whole creating little cracks and crevices for germs and junk to hide. This is why and where I keep finding myself returning to the idea of some sort of painted application. If it's animal safe the urethane porch paint that I used on my wooden shop floor is about the toughest stuff I've ever seen, just don't breath the fumes. Whatever it ends up being I'll have to make sure it gets plenty of sun and ventilation to finish off-gassing before I let the birds near them. More OT, but I'm surprised I haven't read any warnings about the off gassing issue, particularly with all of the OSB and manufactured wood products I see being used in some of these designs. A tremendous amount of our wood products are now coming from overseas, and they don't all necessarily adhere to the same clean air standards being adopted here. Also would warn folks about re-purposing or burning pallets from overseas. Some are sprayed with fumigants to prevent exporting/importing bugs, and some are sprayed with fire retardants, and as someone who has been chemically poisoned and is now hyper sensitive, I take no chances.
Right now my coop design is to be 4'x8' with the 8' side fully accessible by splitting the entire wall into two 4' wide doors for cleaning. Our winters here are never very harsh so chasing everybody out on a sunny day to clean shouldn't be a problem. I'm gonna make the roosts lift outs for cleaning, and cant the floor slightly so I can hose everything out quickly and have it all drain completely - probably about a 1/4" of fall per foot.I hope to cover all of the interior surfaces with the same waterproof material for that reason. My health issues conspire with my natural OCDism to help me over think everything, but looking ahead, I have never regretted over building anything, only cutting corners. Whatever you decide to try, I'd say consider the amount of work the little things can amount to over the years.
I honestly can't imagine our three ducks sharing a coop with our 6 chickens. First of all, the ducks are incredible pigs, and second of all, the ducks are incredible pigs. Our ducks are crazy but a lot more Zen then the ADD chickens, so my duck hut will be a litte apart from the coop, more to keep the ducks from crapping up the coop than anything else. Also want my ducks to lay in one spot, so I'm trying to incorporate a few semi-private nesting boxes in the sides of the duck hut. I know the ducks prefer staying closer to the ground with all of that so I'm also hoping that the 2' climb into the coop will discourage them. Our chickens think our ducks are insane, so I'm pretty sure that if the ducks are acclimated to their hut, the chickens won't go near it, but I'm wrong as often as I'm right so we'll see.
I've seen a lot of chicken tractor roosts that only appear to be about a foot of free space over head, but I would try to give'em at least a foot and a half. If I had a dark colored, uninsulated, roof and anything less than optimum ventilation, I would probably make it even more since hot air rises and pools along the ceiling VERY significantly. Hold a thermometer up near the ceiling in your house and then down near the floor. On the second floor of a two story house runnin' A/C in the summer I've seen as much as 20 degree variances once poorly insulated attic gets super heated. Likewise in the dead of winter when we have the wood stove crankin' it can be 20 degrees or more hotter at the ceiling than at floor level in our house.
This is why I drive my wife nuts. Her dad kept chickens his whole life in a creaky falling down wood slat coop with a dirt floor and some straw with no worries. To each his own I suppose.
One last thing, I also just started reading up on DE and it looks like it can help in innumerable ways, so you might wanna look at incorporating that as well. Good luck.