[JRTJH]

IMO, if you lay the door over a 2x4, apply pressure at the top and bottom of the door, you "MIGHT" stand a chance of breaking the glass. If you lay the door over a 4x4 and apply pressure at the top and bottom of the door, you "WILL" probably break the glass. It's a matter of using a "comb to fix your hair vs a rake to fix your hair"....

On the other hand, if you lay the door on a 2x4 and push on the extreme top/bottom of the door with or without the window in place, you likely will bend the "weakest part of the door" (the area where you removed the window and left only 2 thin edges), so it's more a matter of "sizing up the area that needs to be bent, applying pressure along that area and gently forming it back into shape....

I agree, if you leave the window in place, put the door on a 2x4, have your DW stand on the bottom and you "jump on the top" then hell yes, you're going to break the window.....

On the other hand, putting the door on that same 2x4, (window or not), putting your knees 18-24" below the lockset on both edges, and leaning over the door, use your hands on both edges to apply your upper body weight to the frame, increasing the weight as the aluminum yields and straightens.....

Well, hopefully you get the idea, it's not a "drive on it with a tractor and make the damn thing bend" rather it's a "think about what you're doing and reform the door with the appropriate amount of weight to "caress" it back into shape.....

So, to that end, it's probably of no consequence whether the door is in the window or removed. Now, if, after trying to bend it and feeling that more weight/stress will be needed, I'd probably remove the window rather than risk breaking it. It depends on what needs to be done once the project is being done.