[Quoth]

Editing out the spaces manually doesn't work.

This works:
Delete all the embedded font files.
Delete the URLs in page.csss
Use Embed Fonts in Editor, which imports them with no spaces in the file names, unlike the GUI option on Look & Feel.
Subset them
A fonts.css is now added, so go to page.css and delete the now duplicated font entries. The html files will now automatically have fonts.css

Works on Kobo Libra.

Calibre is finding the required fonts when using Embed Fonts in the Editor apparently based on name in the CSS classes using them and sourcing them both in the normal system wide font directory and my local extra fonts in ~/.fonts (where ~ means home directory). Obviously the GUI option to Embed fonts is doing something odd as many of the font file names have spaces, they don't when added in the Editor.