The glitches:
line spacing of commands in customize mode
size of mini titlebar when prefs/customize active:
The cause:
Made a 'toolbar spacer' iconset consisting of 1 blank icon at 48px and 64px, which when placed on horizontal toolbar will increase the vertical spacing, which works, except it is also causing the above glitches.
I don't see any glitches there? If you use a large icon set, you get large icons. Don't use one if you don't want them.
Maybe you want the spacing options under Preferences / Toolbars / Appearance instead, if you just want to make your toolbars taller than what's inside them.
Yeah this is a glitch, the mini-toolbar wants to make itself the same height as the window frame, but when it's displayed outside the window there's no point doing that. We'll fix it in the next beta.