The published requirements for entry to Canada are the same for both ground and air travel, the only difference is timing requirements for the COVID PCR test. For air travel it is 72 hours prior to departure of the flight to Canada. For land entry it is 72 hours prior to presenting yourself for inspection at a port of entry.Perhaps because the requirements are different for fliers than ground crossings? Victoria Clipper is returning 4 days a week, Fr-Mo, probably to “test it out”.
That is different from current US entry requirements. Air travelers must have a negative COVID test within 3 days of flight departure. Land entry requires nothing, except being a US Citizen or permanent resident.
The following is pure speculation. I can see CBSA having an issue with the fact that Immigration inspection doesn't take place until you are well into Canada. Some people won't meet requirements. There inevitably will be people who don't bother researching what the requirements are or think they can finesse it, or just didn't get their test results on time. CBSA can't just say "turn around" and send them back across the line, they are already well into Canada. All things being equal there will probably more of them now than pre-pandemic since requirements are higher and are more involved. They have to do something with those people and they may not have the same levels of facilities to deal with them that they do at YVR. They need to figure out ways they can deal with it. I can think of several ways, including requiring Amtrak inspection of the ArriveCan information on or shortly after boarding much like airlines must verify documents at check in, reducing the number of ineligible people reaching Canada. Moving the Immigration inspection to the border until the heightened pandemic requirements are lifted, which would be a really crappy option. They need to negotiate with Amtrak but they'll be pretty much one sided. CBSA had the full force of Canadian law and the Canadian government on its side.
Remember, too, this is the agency that delayed and nearly derailed the second train because they didn't want to staff the station for it. It took Vancouver and the BC provincial government howling to Ottawa to get them to do it. Hopefully restoring service won't require that kind of escalation. Especially because my understanding is a lot of Canadians are unhappy with the border being reopened and the Canadian government is really unhappy that the US did not reciprocate opening the land border.