On new reports, with a custom theme applied, a number of visual settings are ignored (eg the fallout value font) and a default 12px uniform padding on the multi-card layout is applied. There seems to be no way to correct these. There may be other settings, these are ones I’ve found so far.
Note that on old reports with the theme applied, or the theme re-applied, this doesn’t happen and the theme works as expected with all settings applied as configured in the theme file.