Air travel is effectively harmonized and bus travel is irrelevant. Vaccination is not required to travel on Amtrak but is required for train travel in Canada. Who enforces that? Does Amtrak check status and offload non-compliant Cascade passengers in Bellingham or just wait until restrictions ease before resuming service? The latter makes more sense.
Amtrak can require an ArriveCan result code of V (Vaccinated but documents require checking) or I (Immunized, no further check required) be displayed either on the ArriveCan app or by paper printout, just like requiring a passport other valid travel document.
Vaccination proof is submitted with ArriveCan application. CBSA does the validating to its satisfaction and determines the result code.
That is what the airlines do, since ArriveCan is required of everyone heading to Canada.
Those without a valid ArriveCan result code can be deboarded in Bellingham, just like people ticketed for Canada without a passport were before all this started. Amtrak conductors made sure all passengers proceeding past Bellingham had a valid document for Canadian entry.
Doesn't really sound like you ever rode the Cascades pre-COVID, and so are unfamiliar with the procedures on it. Deboarding at or before Bellingham or refusal of boarding was normal for those without proper documents to cross the border.
You didn't need a passport to ride Amtrak, either. But you needed one to ride Amtrak to Canada. ArriveCan is just another required travel document.
No "harmonization" is needed any more than for airlines, just a process.