2x wpa_supplicant - its not an issue - you can ignore that (I think - I may live to eat these words, but so far I think its correct).
Seeing the wpa_supplicant for the AP mode - will not make any impact while the interface is not up.
OK at the moment I believe that the issue with the WiFi may have beeb improved with some changes to Raspbian, but the majority of the problem was that the initial random entropy was not available and *everything* that depends on randomness could have been impacted *now fixed in RC7*.
That combined with the recent work to improve the country setup for WiFi (fixing some issues with 5Ghz WiFi) should make for a better experience all around.
Early testing on my Pi 3A+ suggests that AP mode now works like it is supposed to more often than not, WiFi generally works well with one key exception.
If you boot the Pi, and it starts AP mode, and you connect to that to setup the WiFi - and you just reboot it when done, for me that results in broken WiFi quite repeatably

If I do the same thing, use the AP to setup the WiFi and then shut down the Pi, pull the power and power it back up - it seems to work reliably.
With the *very* short amount of testing I have done so far this all seems to be a decent improvement, I'd like to debug the issue on reboot, but that one might be very hard to find!