How can there by an inter-State supply u/s 5(5) when supplies are covered u/s 9(5)

An intra-State supply or inter-State supply must be determined based on the location of actual supplier and place of supply. Tax payment under these provisions merely require the ecommerce operator to deposit tax, but the nature of supply will still be determined based on the actual supplier.

(ICAI FAQ PUBLICATION 06-09-2017 REVERSE CHARGE: FAQ NO.50)