I have Substance Designer 12.1.1 build 5825
When I use such scheme
input bitmap is in .exr format (32bit float or 16bit half-float)
panorama Rotation (all parameters are at default values)
blend node with subtract option - there are differences, but the images must be the same!

Under differences I mean histogram Used Range values (see below)

They are quite big (maybe with this current image), but this is math: if no changes - there must be no difference.
If I connect input bitmap to both blend node inputs that range is 0;0, and that is correct.

The same error persists in any different resolution and with .hdr format images.
Only one thing I've found so far - when inserting exposure node just after the image and make exposure lowering - the error gets smaller too, but it is not 0 in any way.