Cryptanalysis in a blackbox setting using deep learning is powerful because it does not require the attacker to have knowledge about the internal structure of the cryptographic algorithm. Thus, it is necessary to design a symmetric key cipher that is secure against cryptanalysis using deep learning. Kimura et al. (AIoTS 2022) investigated deep learning-based attacks on the small PRESENT-[4] block cipher with limited component changes, identifying characteristics specific to these attacks which remain unaffected by linear/differential cryptanalysis. Finding such characteristics is important because exploiting such characteristics can make the target cipher vulnerable to deep learning-based attacks. Thus, this paper extends a previous method to explore clues for designing symmetric-key cryptographic algorithms that are secure against deep learning-based attacks. We employ small PRESENT-[4] with two weak S-boxes, which are known to be weak against differential/linear attacks, to clarify the relationship between classical and deep learning-based attacks. As a result, we demonstrated the success probability of our deep learning-based whitebox analysis tends to be affected by the success probability of classical cryptanalysis methods. And we showed our whitebox analysis achieved the same attack capability as traditional methods even when the S-box of the target cipher was changed to a weak one.