Why is that, when the Mastercycler display shows that the temperature (e.g. from 72 °C to 94 °C) has been reached, the cycler still doesn't begin with the new step (time counting)?

IMPORTANT: The Mastercycler display shows the block temperature, i.e. the temperature registered by the sensor. You have probably set ""Tube Control"". Since the temperature in the sample is attained later than the temperature in the block, time counting begins at a later point, i.e. when the temperature has been reached in the tube.

Is the block temperature overshot or undershot even when "block control" has been set?

No. The block is heated above the programmed temperature (or cooled below the programmed temperature) only when "tube control" has been set, so that the desired temperature for the sample can be attained more quickly.