Its very straight forward as of this past summer, but a different process in each direction (i.e. when to call in, when not to)
I am a firm believer of the fewer humans you deal with, the better off you are.
I'm with you on both of the above.
On the Great Lakes this summer it was like you say, slightly different in each direction.
Going into Canada (as a US citizen):
Canada said you should go to a place where they have one of their special phones (so NOT at anchor), and then call in. But what I found out was that some (all?) of the special phones no longer exist, and so you just call on your own phone (but you still are supposed to be at one of the specified land places, I suppose so they could come board you if they wanted to).
Coming back into the US (as a US citizen):
I had a few different answers on this one, but basically you are supposed to use the CBP Roam app on your phone or tablet, and you check in via that. (Or some marinas supposedly have a tablet you can use.) I had read that you could be anchored (and I wasn't even near anyplace with a marina or town in my first US anchorage), so I checked in that way. Tho it asked for the address of the marina I was at. It also asked if I wanted to be a "preferred traveler" but I said no thanks. (Didn't know what that was and wanted to at least look it up first.)
They called me (somehow we couldn't get video call to work, probably my fault), and I asked if it was okay to check in from an anchorage and they said yes. Very friendly and helpful.
Later, I got a message that said "Welcome to the Preferred Traveler program, now you can check in while underway or from an anchorage." Go figure. This is not anything special like Nexus though.
I did one more over and back (different locations) and it went the same as the first time in both directions, except CBP roam didn't even want a video call, just said "enjoy your stay" and gave me an entry number. Which kind of made me laugh because I thought, Why thank you, I'll make sure to 'enjoy my stay' in my own country."
BTW, this all went in accordance with what I had read in the preceding month (researching). The only two differences were the fact that the Canadian phones were gone (but you still had to be in one those locations). And the CBP thing about the "now that you are a preferred traveler you can check in from anywhere" which I didn't now about (thought you could always check in from at anchor).
I think there is a decal or similar that you need to get when entering the US if you are over a certain LOA. I was under that so don't remember the details. I think it was like $25.