I think most of the views through the front windshield looking into the cockpit were done on a gimbal that held the body of the replica(?) in the air off a cliff at the southernmost point of California (Point Vicente), with the full horizon view of the Pacific Ocean behind it. Nolan and another guy turned and rotated the cockpit while mounted cameras filmed. Some other shots that were done there were the closeups of Farrier's landing gear being cranked down.
Some other filming through the front windshields was done with the replica in the water (the scenes where Collins (who is shown above) is sinking in his crashed Spitfire. The picture you posted of Collins may be the view we got of him in the cockpit when his plane was sinking.
The IMAX positions I saw for flying were with IMAXs mounted to both wings, one looking sideways into the cockpit and one looking forward along the fuselage. In addition, they sometimes flew with an IMAX that had a custom long angled "snorkel" lens that went over the pilot's shoulder and could be controlled to look in different directions, just as a pilot would.
The IMAXs could only hold 3 minutes of film, so from multiple airports in at least 3 countries (France Netherlands and England) they had to repeatedly take off, film, land, change film (camera configurations could have also been changed depending on the shots they wanted to film).
Skip to about 20 minutes in this Dunkirk Spirit making-of Documentary and you can see how the cameras were used on the wings, the snorkel lens, and the shots that were done on the ground:
[youtube]
http://www.youtube.com/watch?v=qw0G_ddYoPs[/youtube]
As someone said above, the angle of shooting (angle of lens vs angle of the windshield) could get reflections of the camera out of the picture. Also, in general photography, a polarized filter can be used to reduce reflections:
https://photography.tutsplus.com/tutori ... photo-1398
And people can wear dark clothing or camouflage to hide their reflections in ground shots.