This is an annoying bug, and makes it nearly impossible to look at some variations. Its been known about for ages so why is it taking so long to fix it? Especially when its easy to fix - just grey out the sync button - or leave white space there - when its not needed, or just shift it.
In Analysis mode, the third row of buttons is moved left and the Back To Game button is added to the end of the row, rather than putting it below the third row, like the sync button, so why not just put the sync button in the same place.
Personally I think the layout of the buttons could be tidied up a bit. There are two possibilities.
First you could shift some of the buttons from the first to the second row and make two rows with the same length and a third, shorter row, with room for the sync/back button. Or you could shift the second and third rows left and leave a large white space on the right and put the sync/back button in the middle of that space - at a level in between the second and third rows - giving it slightly greater visual prominence than it currently has.