Sorry, you are right.
If you deploy first from the new IDE, no problem.
But if you first deploy as a web app with the old IDE, then deploy from the new IDE, it will indeed create an entirely new deployment, with a different URL.
As you've seen, you now have 2 different "active" deployments.
If you go to the old editor and click on "Publish" > "Deploy from manifest", you should see 2 deployments in addition to the "Latest Version (Head)" one.
- A deployment named "web app meta-version" => that's the one created from the old IDE
- another one named "default meta-version" => created via the new IDE
Currently, the "New deployment" menu in the new IDE lets you update the version linked to the "default meta-version", not the "web app meta-version".
I tried to rename the deployment "web app meta-version" to "default meta-version" but it doesn't help.
For now it seems you'll have to wait for an update in the new IDE before you can update your web app while keeping the same URL.