Yeah, blender's snapping function can sometimes be a little tricky so wondering if you tried snap to vertex whilst toggle X-ray to on or edge/vertex slide? (shortcut G x2) Personally I've found most of the time works when an asymmetrical edge doesn't align as expected.
Don't know if there's a way to slide things to match an axis if you have an off angle edge? For example, I want to align this loop on a sloping section to the y-axis of the perpendicular box, however it snaps a few units off. Am using the following snap controls This is for a project where I'm taking old BSP level geometry…