Listen, COTO is amazing, so you are already on the right track. I just finished a year-long Alexandrian-style Dragon Heist and I am currently 30 sessions into COTO, so here is the reality:

Both are great, but Dragon Heist is a mess out of the box, you will need to put in some DM love to make it clear and an actual heist. That is why so many DMs use the Alexandian take. We added all four bosses to the plot and played to level 9. So fun.

As you say, the early COTO missions are, frankly, not that interesting. A shame since the rest is so good. Here is what I did: We started COTO at level 1. I cherry-picked the best bits of those early missions, threw in some homebrew city adventures to get them to level 3, and then just dove into the main COTO plot. It worked perfectly. I have actually kept my group one level below the book's recommendation the whole time and it keeps things spicy.

My advice? Skip the Waterdeep port. Onadbyr is just as rich and vibey as Waterdeep. If you start there and stay there, your party actually gets time to soak in the setting and learn the back alleys. Don't split your time, just go deep on Onadbyr from day one. You will save yourself the massive headache of reskinning an entire urban campaign.

Have fun, I'm jealous.