I have taken a look at this and it seems to be a limitation of those themes.
The ones with an issue are using the shutdown button shift code to move the button a somewhat large distance.
If an update is now pending the button is longer as the text is longer. On skins which don't use this or barely use it, there is no problem. Things fit correctly.
The shifting logic was intended only for moving the button away from say a border on the left hand side, not to try to simulate things being centred.
The best solution we can offer is for it to also apply the left hand shift to the right hand side and if there is insufficient room then expand the right hand side. Be aware that some themes may not like this but if they don't then they probably also don't work well with higher dpis.