@NotMyFault
Thank you for doing the checkerboard test. Certainly proves that the issue still exists. Although, this should have been completely resolved. There is an application named PTGui which doesn't loose quality if the projection is changed, which is why I will now have to use that till the issue is fixed in Affinity Photo.
Its really a deal breaker for me.
The only main reason I preferred Affinity Photo over other softwares is that it supported 16-bit RAW files in equirectangular projection which Photoshop could not.
Now when I know that using Equirectangular Projection, even just once also degrades the image quality, I would have to remove Affinity Photo from my workflow. 😓