I don't think it's a stupid question. I had the exact same issue with my Tiger 2 I'm building. The fact is that 1 degree, and even 2 degrees is a very small measurement. If you really think these small numbers would make a significant difference, the thing to do is to make some drawings as accurate as you can with a protractor, and then try to get it as close as you can. You can either add a shim (washers, usually) under the engine mount, or mount the engine to the mount slightly crooked.

The purpose of down thrust is to keep the plane trimmed at different throttle levels. (In other words, to allow the plane to fly level at different speeds without you having to adjust the elevator.)

I would guess that a lot of modelers just mount the engine square to the fuse, and don't even know the difference.

--Mike