**Use different wpa_supplicant files** in [How to set up networking/WiFi](https://raspberrypi.stackexchange.com/a/37921/8697)
describes how to setup networking to use different wpa_supplicant files for each interface.

Your `etc/network/interfaces` should work (only because it causes `dhcpcd` to disable itself) and can be configured to use multiple wpa_supplicant files, however this uses old Debian networking, which is far less robust than `dhcpcd`

There is no guarantee which interface will be assigned to wlan0/wlan1 due to a race condition (although the onboard WiFi  will probably win). To be sure you should enable  **Predictable Network Interface Names** (this is used by most modern Linux OS).