If you're adding buildable canals, will you be adding buildable straights as well? Like, allow a country that controls both southern Iberia and northern Africa or southern India and Ceylon to construct a system of ferries and whatnot that'll end up functioning just like 'natural' straights.
I think you've stumbled on something here.
Prior to this Gibraltar has always been made separate from Africa on the map, because otherwise Spain swallows Africa most of the time. But if a strait has the requirements of a canal, the balance issue with Spain appears can be adjusted down to become something that only happens occasionally, if ever, when the AI is playing.