That’s a nice design! It should all be possible.
The values you highlight are not hard-coded - they are computed by the lumino layout dynamically based on the CSS styles. In your particular example of #jp-top-panel it comes from min-height which can be overriden in theme extensions:
A very few values are hard-coded and those should be changed (contributions via pull requests welcome).
Note: there is a template for theme extensions and a theme editor which might help to kickstart theme creation (also see this blog post). Perusing some of the existing themes on GitHub and on PyPI can be helpful too.