Your comments

Fixed in v4.4.5.
Sorry for the inconvenience.
That's already possible with the advanced option "no_width_limit".
See help file, Advanced options -> OptionsEx for more details.
That's already possible with the advanced option "no_width_limit".
See help file Advanced options -> OptionsEx for more details.
Done in v4.4.4 as an advanced option.
No, it's not possible to blacklist elements, the change is global.
That's not a bug of the tweaker. The extension probably assumes that it's tray icon is of a particular size, so it behaves differently now that it's smaller.

You might want to contact the developers of this extension, if it's still maintained. This should be an easy fix, as getting the padding is easy and is documented (using the TB_GETPADDING message). Also, the Shell_NotifyIconGetRect function might be useful.
Of course it has nothing to do with grouping, that's just a screenshot that I had on the server already :)
I'm glad you figured it out.