If $k$ numbers are chosen without replacement, every set of $k$ numbers has the same number of arrangements, $k!$. So for this sort of question you can ignore the arrangements without affecting the probability. One way you say there are $12$ pairs of numbers with minimum less than $4$, and $15$ pairs total, so the probability is $4/5$. The other way you say there are $24$ arrangements with minimum less than $4$, out of $30$ arrangements in total, so the probability is $4/5$. This works because all the possible arrangements are equally likely and all possible sets are equally likely.
If the numbers are chosen with replacement, say by rolling a die, not every collection of numbers has the same number of arrangements. In this case it is vital to count arrangements, because it is the arrangements (not the possible collections) which all have the same probability. So with replacement there are $27$ arrangements out of $36$ which work, so $p=3/4$. It would be wrong to say there are $15$ collections of numbers which work, out of $21$ possible collections, because these collections are not equally likely (it is easier to roll a 1 and a 2 in some order than two 1s).