The Format>Staff Space value affects vertical placement of tablature numbers

Indeed. As far as I could see after a quick check, this is a regression from the first version 3.0.0.
Feel free to report this in the Issue Tracker.
Nevertheless, as workaround, you can easily compensate by doing: right-click the TAB staff -> Staff/Part properties -> Advanced Style Properties -> Fret marks -> Vertical Offset: change to negative value (for this case), for example: -0.20sp
And you get: 1Staff Space setting affects vertical placement of tablature numbers.mscz

I'm fairly sure there is an open issue for that, but I can't seem to find it. Surprising it doesn't come up more often.