Looks good, I still need to test.
Couple notes:
I call the asset "dialog" instead of joomla-dialog, because, well, it joomla already, like we have 'core', 'showon' etc ;)
I would prefer do not to have an extra css, it is very basic, I would do it as part of main template.
For width and height, would use default (defined by css) to keep all popup in consistent size, and set it in script when it need to be diferent.

I call the asset "dialog" instead of joomla-dialog, because, well, it joomla already, like we have 'core', 'showon' etc ;)

I renamed them. I think it would be a good idea to have a system/ui folder and get also all the custom elements from the other repo here. I mean if there's a way to move the docs and the tests there's no reason to have multiple repos

I would prefer do not to have an extra css, it is very basic, I would do it as part of main template.

I disagree here. The script should provide some basic styling (mind I didn't copy everything from your PR, only the CE parts) and also the template has the ability to override the assets. Also we're doing that with the alerts and tabs..

For width and height, would use default (defined by css) to keep all popup in consistent size, and set it in script when it need to be diferent.

Removed them

The script should provide some basic styling

That is true, originaly I also wanted to do a separated css, but then I realise that the basic styling already comes with native dialog element ;)
Well, I know it is ugly, but it is usable. There only issue is iframe sizing.