Lyman I'm not sorry you raised this question, it's a good conversation!
I agree with stating the measured distance on both map and cert (use small print on the map if you like!). They can still call the course a 5K I would think.
As for the 5003 m course, Mark, I think I'll go back to my suggestion that we start at 2 x SCPF. In other words 5003 m doesn't need mentioning for the reason you already stated-- but if it's 5005 I think, if we trust our measurement system, that we know it's likely to be more than 5 km by something on the order of 5 meters. I'm assuming they already increased their "raw" constant by adding 0.1%, so a "5.005 km" course was actually measured to be 5.010 km.