This is a floating point error, and likely not something you need to account for.
Your pipes will be installed in hangers which are off by more than that value. In fact, as a test try and draw that 0.000003 degree angle, and get the rise over 100 units - the difference on the X axis is something like 0.00005 units. If you are in meters that is 0.05 mm, something you wouldn’t be able to measure. and that is with a 100 meter long pipe no less.
If you are really worried about it, there are a few things you can try:
Normalize the vectors before you take the angle comparison.
Rotate the object twice.
Utilize the RevitAPI’s ElementTransform tools to set the rotation and apply an alignment when done to confirm they are the same.