This is the way I see it and although it may sound weird, to me it makes sense.
Its very possible that the AoC has met both Harry and Meghan (both separately and together) and has had conversations with them. Sometimes it only takes a short while to get a "feel" for a person or a couple. There are many, many beautiful souls out there that have never stepped into a church or joined any denomination but yet are very attuned to their spiritual selves. Clergy like the AoC would definitely be a person who would pick up on these kind of things.
I think he's found both Harry and Meghan to be truly dedicated to each other and that the wish to marry in the Church of England isn't an empty one just keeping up a tradition or doing it because "that's how everyone else does it". Its something this couple truly want. Meghan wouldn't be going through the process of being baptized and confirmed as its not a necessity but its something that she does really want to do.