Disadvantage of the bottom being left open will only be seen if you have good flow under the vehicle to begin with. Do you have a full belly pan?
I would build directly off the hatch if you have a spare one. Building it this way will let the hatch and kammback open together.
Materials can be a wide range of things... How long do you want it to last?
1) I built my SedanKamm out of a used campaign sign that was made of coroplast. It was very appropriate for the build, and will last a long time even if it's exposed to constant rain/sun/ etc. Coroplast is easy to work with, and easy to come by, just call your local sign shop and ask for prices of both new coroplast, and used coroplast. New it should be about $20 for a 4'x8' sheet, used it is sometimes free. If you get used that has been printed with vinyl, you can take your time and peel the vinyl off (tip, let it sit in the sun for a while and heat the adhesive). If it's campaign season near you, look for guys with big 4'x8' signs, and offer to help take down, and dispose of, their signs after the election. If you find ones that have full color printing (a person's face), it's printed on a large piece of vinyl that is easy to peel off. Mono-color, or even multi-color signs are typically colored vinyl that is cut and applied, and takes much longer to remove.
2) Lots of the big signs are actually Alumalite, which is thick coroplast that is sheeted on both sides with a fairly thick aluminum. This stuff is really rigid. We worked with some, and a guy offered to bend it on his 30 ton sheet metal break, but after seeing it, he decided it was a bad idea! Sharp edges can cut right through heavy leather gloves... ask me how I know. Be careful if using this stuff!
3) There is another sign making material that is aluminum over a foam core. This we did bend on the big 30 ton press, but the operator refused to do more than a few degrees at a time, and would only bend it in the 4' direction. 3 grown men could not make the stuff bend over a 55 gallon drum.
All three of these options come in multiple colors, which you will get to choose if buying new, but have to put up with what you find if getting it used. I don't think I have seen brown for matching your car, but I have seen black, which is pretty stealthy.
4) For windows I used thin acrylic sheet (Plexiglas is a brand name of acrylic, Lexan is a brand name of polycarbonate). I got mine at Hobby Lobby for under $5 by using a 40% off coupon (which they have about every other week). I got the biggest one, and sized my windows to make a single sheet make all the windows (and a grill block for my wife's car). The thin acrylic worked well as windows on the SedanKamm, but worked very poorly as a grill block (rocks go straight through it). Coroplast, on the other hand, makes an excellent grill block, but that's another story.
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