First I would rename the wpa_supplicant.conf file to wpa_supplicant-wlan1.conf so that it should not apply to wlan0. (wpa_supplicant.conf is a default file that could apply to any wlan adapter.)
Hopefully the wlan0 interface will be still unconfigured when hostapd tries to take it over.
If that doesn't work correctly I would check that wlan0 and wlan1 don't exchange places upon reboot (and hostapd would fail because some options are not compatible with the other interface.)
If this is the case you can either enable "predictable network interfaces names" (via raspi-config?) or whip up a udev rule that gives one of your interfaces a specific name. AFAIK it's one or the other options.
PNIN for USB is lame, the name you get is the MAC address with a prefix. It won't change upon reboots, but it is quite ungainly and impractical.
On a Pi eth0 is a USB device so its name will change. wlan0 on Pi3 is an SDIO device, I don't know what PNIN makes of it.
See DougieLawson's post just below.