In your question, you already pointed out, that the necessary condition is
More generally largest prime minus one does not consists of smallest prime as a prime factor
therefore, it is sufficient to just check if $p$ divides $q-1$ by computing division. You can just verify this condition during the key generation. I don't know of a more efficient way.
However, in general I think that the security of the scheme depends on the size of the smallest prime, however, the efficiency depends on the size of the obtained modulus $N = pq$, therefore it is probably reasonable to just use equal size primes for the best security and efficiency. I can not point out any schemes that require equal length primes.