What are the reasons for prohibiting borrowing from commercial banks and for analyzing the same transaction with Islamic banks, given the similarity in their objectives and mechanisms? Does borrowing from an Islamic bank negate the causes for prohibition?

Islamic banks do not lend with interest. Any bank that lends with interest has fallen into clear usury, and calling itself "Islamic" does not benefit it. Many people do not differentiate between permissible and impermissible transactions, so they assume that what an Islamic bank does is exactly what an interest-based bank does. However, there are differences that affect the Shariah ruling.