EGR - always a warning?

More likely the opposite, my 2 cents. Any time past 100K miles you really want to get on it.

This is for your 2010 Prius I assume? Prius c doesn't have such EGR, I've reported, mod could move.

 

It's possible that the built-in test for EGR flow might not happen as often as it was originally designed to, if the software to do it was just transplanted into a hybrid design that doesn't often reach the engine conditions where the test was programmed to run. That's speculation on my part, more on that here.

That could be an argument in favor of now and then doing essentially the same test deliberately with Techstream, as described over here. We don't have enough data collected yet to be able to say X is a good result, Y is a bad result, but that's the reason for collecting it, and we have more now than we started with.

 

The first post here:

Intake manifold EGR ports clogged - PICS | PriusChat

by @ArmyChief has a pdf with images of the intake manifold EGR passages (one per port). The passageway for cylinder #1 is pretty much stoved-in with carbon, at 156K miles. The passages get progressively cleaner, going from cylinder #1 to #4. FWIW, Cylinder #1 is often the head gasket failure point (mentioned here, also in a Gasket Master's video).

In the link above I don't believe @ArmyChief mentions warning lights or codes. He might see this and comment.

 

i would say rarely. the first message is usually lost coolant or rough engine