Yes, you have a Canadian-released copy. I don't have a box for Bonk 3 but my copy of Darkwing Duck has a UPC sticker over the original like you describe. It probably safe to assume that a different UPC code was needed for all Canadian releases and all the boxes have stickers.
In Canada, the foldout manuals were included in all of the late period Turbografx releases (the twenty or so games without jewel cases). Older games came with full-fledged, stapled manuals in both French and English. Apparently they were trying to cut costs by the time the last few games were made. No one has ever talked about the UPC stickers on these forums but the Canadian manuals don't seem to be particularly rare. Sometimes a few French manuals are sold around here and they usually go the same price as English manuals, regardless of whether they're foldout or stapled. French manuals are somewhat uncommon but their lack of use for English readers seems to offset any increase in value.
I have foldout manuals for Bonk 3, Darkwing Duck, and probably some others.