I'm looking at doing the same thing in my house later this year. But, I want to emphasis that drilling through your windows/window frame can void your warranty. If these are new windows, you'll want to have that warranty in place just as an "what if" happens in the near future. You'll have to refer to your warranty documentation to see if drilling will void your warranty.
The Ademco 3/8" Diameter Miniature Press Fit Magnetic Contact looks pretty standard. Just to be on the cautious side, you can always measure your frame to see if you have enough space. Otherwise, I see no issues with installing these on your door and the frame. Also, I've seen them installed on the top of the door or the side of the door. That's your call.
You may want to re-consider and utilize non-recessed/surface mounted contact switches for your windows and its frame. First of all, research more about your windows. If they contain spring mechanisms in the inside of the window or the window frame, then you will not be able to drill a hole. Otherwise, if there are no physical obstructions, then you can normally drill the required diameter near the bottom of the window. You want to make sure that the hole is covered and not exposed to the outside environment. If exposed, you could use some sealant to protect the contacts. Also, if your windows are double-hung, you'll need contacts installed at the top and the bottom of the window. You can connect the two contacts in a series so that you don't have to run two sets of wire to the control panel.
All the recessed options you provided are for different scenarios of windows/doors. Normally, regular sized contacts are used except where these sensors may be too large to fit the door or window frame. Stubby contacts would be used in such occassion. The stubby/earth magnet contacts are great for window applications because of the size of the magnet (depending on your window type, you may not need to drill into your window to fit the magnet).