I have european equivalent to Z150BH (F50BT) and have the same issues:
I think is the pioneer app which cuts the GPS signal, not the mhl adapter.
With the mobile gps turn on and pioneer app launched, as you said, waze gets no signal. If I exit stock app (with "Track -" button or with mobile back button) I watch in the HU screen my mobile mirrored but no touch control. Using the mobile, I launch "Navigator", for example, and it uses GPS mobile signal without problem (note at this point the mobile is still connected to the HU by the mhl adapter).
If I switch to Waze, as it's an app binded to the pioneer app, I get touch control but I lose GPS signal.
All this refering to the mobile GPS signal.
Refering tho the HU GPS signal, I've send an email to Pioneer's customer service asking why I won't get signal using theirs stock app.
This is the answer from Pioneer:
"The AVIC-F50BT has embedded navigator, with built-in GPS antenna. When
using a navigator App, GPS antenna used is that of
smartphone, so you will need to have the smartphone in a place that receives
good GPS signal."
As we know for the tests we have made, this is false. So I've send a reply but without hopes of getting a satisfactory answer.
I think the only way to get Waze working is waiting to an ARL release which works in our devices.
I'm using appRadio Mode with an Samnsung SIII which is not in pioneer's compatibiliity list.. Has any of you this GPS problem with a smarphone supported by Pioneer?