I'm not sure of the rates from Newfoundland to Canada in 1897. A registered rate would be a bit more. And a heavier cover would be double rate plus registration.
If I was thinking that there was a stamp added, I would guess the light brown stamp was the added stamp along with the thinner, lighter cancel. Because it looks cleaner than the darker stamp. Notice how the darker stamp is a little soiled on the white part of the stamp. But the light brown stamp looks clean and newer. Also, the dark ink on the right stamp looks closer to the shade of black of the ST. JOHN's oval postmark.
I can't say I'm an expert on postal history so I would take my remarks with a grain of salt. Now that you have it posted, maybe you can find out some good info on it. Your covers all look quite nice and interesting. I have some covers that are in this grey area, too.
Here's a Hechler philatelic cover that has older stamps posted in 1896 which proves that collector's were making these nice covers at this time. Different colour paper on these two stamps also.

