That is true, but it did not bother anyone, because fast long-distance communication either did not exist or was very limited (e.g. smoke signals) and syncing of clocks wasn't necessary in everyday activities; for a medieval person, the idea that clocks in Vienna and Prague MUST be synchronized would be as strange as for us the idea that everyone in the same city should have their breakfast at the same time. It just did not serve any obvious purpose.
There are only two exceptions I can think of.
a) people doing astrological horoscopes for someone who was born in a different place (a big thing among some nobility and royalty) would probably be bothered a bit by the time difference,
b) armies trying to converge on the same target at the same moment.