True mahogany is a good choice. It is highly resistant to rot. But many fakes exist. They do not have all the desired properties of true mahogany. Here is a link that might be useful: Shorea

Never order a door that needs to be stained or painted, it should always be prefinished at the factory by the manufacturer.

Mahogany is used as it is a great exterior wood as it is used in boat building. Can it be painted? Of course it can but covering such a decorative premium wood is not advised by anyone who likes real wood. You can paint it and have the look you want and also have the strength and decay resistance of the wood. A shame but its your door and you will still have to repaint every other year anyway so the maintenance will be the same. I would never paint paint it as it is such a shame to cover that beautiful wood grain. Look into Waterlox it is great exterior coating. ANY exterior paint, coating, clear, etc will require maintenance end of story. DO NOT slap on a HD polyurethane as it will flake and cause all sorts of issues on a front door. Mahogany will change color in the sun. Staining with another wood color again makes zero sense. If you wanted a chestnut or hickory you should have just had the door built out of that wood. I can never understand people buying one type of wood and then saying they want it stained the color of another but this question is asked daily. Look into UV dyes. the dyes can tint the overall color of the wood but allow its natural look show through. I would us the Waterlox and see how you like it. You can always paint over it but if you paint there is no going back. You are trying to make a $1000 door into a cheap $200 door. With that overhand you should be fine. Plus one of the biggest killers is storm doors that bake the the door as they don't allow air flow to cool the door.

Since your windows are at the lower elevation I would definitely keep the transom. It's about maintaining a consistent and human proportion and maintaining that top of window datum line. Otherwise the front door appears to be dwarfing the rest of your front facade. We have a single 7'-8" tall door on our house but the windows in the rooms on either side have windows which are set just as high.