The dots are there to indicate polarity of the windings.
It's in case the circuit couples the windings together in some way. They might need to be in sync or in opposition, depending on the circuit.
For example some oscillators use inductive coupling between windings to generate a feedback pulse.
Or in case there is another winding which needs to be hooked up in series. For example, in order to double the voltage.
If the purpose is simple step up or down, then it's not crucial whether the dots are at the same end or at opposite ends.