While attempting to test my new elevated rail crossing, I kept getting 'Rail ends well inside blueprint' errors. I eventually determined the problem was that my blueprint, which is intended to tile, included the power pole for the next segment in each direction, so that the power poles within the intersection could connect to them with red and green wires. The tester was including those power poles when calculating how big the blueprint was, then complaining that the rails did not extend to the edge of this bounding box.
I'm almost certain this is a regression; one of the blueprints I attempted to test with this was one I've tested previously.
The solution is simple: ignore non-rail buildings when calculating the edges of the blueprint for the purposes of connecting to it.