GTK+ 3.20 must have landed in Yakkety a few days ago ... or is there another reason the borders and padding and so on are all gone? 
I’m seeing it to. System wide, different themes yield different results. Guess lightdm and themes have some catching up to do.
Yikes! Yuck! 
Ambiant-MATE is being ported here:
So, work in progress. I guess other GTK2 themes may be a problem though.
Yes, what I should have said is GTK+ 3.20 landed before the themes.
From Martin's most recent email to patrons:
[...]
Now the good news! Over the coming days a new Ubuntu MATE artwork
package will land in the Ubuntu 16.10 archive that fully supports GTK
3.20. This has taken some 6 weeks of development effort, which this
Patreon funded
[...]
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Just updated my VM. Looks much better now 
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Thanks for the heads up, going to do the same now 
First thing I noticed
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Not seeing an improvement in FireFox. No toolbar and checkboxes/other things still missing.
Good news is FF49 does not have these issues, so I guess I’ll stick with that.
I don’t think it’s all done and uploaded, but before I didn’t see any button outlines or field border or padding at all in the default theme.
As for Firefox, I think version 48 is the first version with any GTK 3.20 support, but a lot isn’t fixed until 49.
Yep, things are improving
But FF49 is sightly out of focus.
If you on 16.10 mate-hud has been dropped. Testing revealed too many compatibility issues. So please apt remove mate-hud this should help Firefox and LibreOffice behave correctly. We’ll revisit mate-hud in 17.04.
Hud was removed on mine by an update on the 17th of this month.
I can’t change system fonts on mine with either Appearance or Dconf. Is that a work in progress?
Focus turned out to be virtualbox. Focus is fine in fullscreen mode.
FF48 now has the menubar in beta1 (I did a fresh install).