Yes, I compare drugs with drugs, not molecules with drugs.

No. The analysis in the paper above referred to molecules vs the snippet in the fda referred to products. More generally, other than marketing materials to doctors or patients or very rare exceptions talking about formulations etc, the scientific literature refers to the molecular entity as a drug not the particular named/branded product. I hope that the tool you are building will not mix up such concepts.

The link you posted found "1,578 US FDA-approved drugs"(exact citation).

Yes that is the standard language in the field. It does not refer to the number of marketed products. Look up the number of novel drugs approved by the FDA per year. It only recently exceeded 40 per year, and the FDA has not existed for very long.

if we consider that you are not making things up(which I am very not confident), then your link is useless in this discussion, because it doesn't give a sense how many non-protein targeting drugs were approved by FDA.