In the Autokit app config there's an option that redirects all audio through bluetooth, I think it goes something like "Audio channel (beta)" and the options are Bluetooth and Box. That option appears after you let it update; if you just install the apk in the address it will install an older version that doesn't offer that option, so if you updated and don't want it, just delete Autokit and install it again from the original link and don't update.
I enabled that audio channel option and that corrected the problem of showing you Carplay as an audio source in the phone during a call and setting it as default, but the audio from Apple Music or similar then goes through your iPhone speakers instead of the HU speakers.
The problem setting Carplay as audio source during a call, for me at least, was that the mic had something like 3-5% of the normal sensibility, the caller says that they hear me like underwater facing down lol, I thought maybe the box had a mic and couldn't hear me well as it's in the glove box, but my box is the one without mic. Looking at the phone, in the audio source I saw speaker, bluetooth -head unit- and Carplay, and Carplay was by default enabled, so for every call I had to pick the phone up, change the source to bt and only then I could sustain a normal conversation. That Audio Channel option resolved that, but instead created the problem of not redirecting the music to the head unit.
In the end I left that audio channel option in "box" and somehow my iPhone learned that I preferred to use bt instead of carplay as default and is working fine now. But I think it's a messy app, with very unclear options and after all not sorting out all the problems. For instance, for every call, the head unit's bt phone app will lay over carplay displaying that answer/hang up popup over the carplay call screen. When using carplay if I press the answer button in the steering wheel in order to display the call history, that bt phone app will take over, minimizing carplay, unless I'm actually answering a call, in which case it does what it expected. Probably Autokit requires more privileges in order to totally take over as it should, not sure, but when you have native carplay in your head unit the only way out is the exit button, all the rest is owned by carplay.
Well, at least now I have carplay, before buying the carlinkit I didn't, although not working as seamless as it does in enabled factory head units.