What is a proper way to consider the supplementary materials as a reviewer?
Your job is to provide critique and suggestions by which the authors can improve the paper. The published paper should be self-contained; that does not mean that as a reviewer you should ignore the supplementary material.

It sounds to me like you already know how to advise the authors to improve their paper. I would definitely ask them to make improvements and submit a revision, rather than reject — especially if the paper would be "perfect" with your suggested changes.