I finally got a reply from Via Rail customer service. They apologized and said the agents got it wrong, and they will follow up with the appropriate manager. I guess that's just about the end of it.
One other note that's tangentially related to this subject, in case anybody ends up flying due to a canceled rail trip in Canada. Air Canada checks IDs during the boarding process. If you're a US citizen, you need your passport. They wouldn't let me use my enhanced license. Glad I stuck the passport in my bag at the last minute.
Well, glad they admitted it, even though threw a huge wrench into your trip. If Amtrak you may have been able to get a voucher for your troubles if you pressed Customer Relations, in addition to the refund. I don't know about VIA, never having been in that crappy of a situation with them. If there is a return contact on the email, you may able to talk them into something using it. I still think they owe you something more, a least a gesture after they sideswiped you like that, even if it just a voucher or Preference points.
As to the EDL, it isn't good for air travel, period, only land and sea crossings. No airline will accept it, they can't.
The only thing aside from a passport that is valid for flights is a NEXUS card. Even NEXUS cards are rejected or looked at askance by airlines, though AC is one that usually knows the rules and allows them. I've had Delta question my NEXUS, and only the passport works in their check in kiosks, at least in Canada. If you want to use a NEXUS card, you have to check in with an agent, who may still dispute it.
With either a NEXUS or an EDL, carrying a passport, too, is a good idea anyway, as you found out. With NEXUS it is actually a requirement. You may not have to show it, but you have to have it and CBSA is within their rights to demand it.
BTW, NEXUS cards not only give you TSA Pre-check included, they also get you the equivalent for CATSA. They're the only thing that does, CATSA doesn't have a stand alone program like TSA Pre-check.
If you want to use the document requirements source that the airlines use, TIMATIC, IATA has a portal consumers can use to access TIMATIC:
https://www.iatatravelcentre.com/passport-visa-health-travel-document-requirements.htm