So, my main router is a TPLink Archer C1200. I want to use my HaP AC Lite as a WiFi extender (repeater, I can't drag an ethernet cable through the house). But right now my Mikrotik is broadcasting four additional networks, but I only wanted two. One for 2.4GHz and one for 5GHz. Why is my Mikrotik still broadcasting the default Mikrotik SSIDs? I set that _2 SSID just to make sure I'm connecting to the mikrotik instead of my TPLink, I plan on changing that to the first SSID.

Also when I disable the master interface it stops working completely, which I expected.

You broadcast one SSID only per WLAN interface set as AP.
Your client device may still list "old" SSID's, that actually are not there anymore. Trying to connect to them will remove them from that list.