Yes, I have modified that file. And I agree, all new apps should maintain that height, but they aren't (for me at least).
The same file in the new app actually maintains this height setting, but the header controller stays 40px.
I also found [installation folder]\client\stemapp\config.json that has a height setting for the header controller in the widget collection. If I change that setting to 80 and create a new app and open [install folder]\server\apps\[app number]\config.json it is back to 40. But if I change it to 80 in that file after the app is created and launch the app again it actually changes. It is either getting overridden somewhere else during the creation of the new app, or never comes across.
Could it be hard-coded into the building code?
Jeff Ward
Summit County, Utah