What vehicle year? Only supported on the 2016-2017 Pilots. Not surprising about the Netflix. It's not a listed supported option and in most states it is illegal to play videos etc. on the front console in view of the driver.
Disclaimer - this is your vehicle you are messing with. If you are not comfortable with potentially permanently damaging the head unit, stop here. Now for the good stuff. Credit where credit is due: this method relies on the recent "dirtycow"...
So the trick to getting the Waze audio to play correctly on top of radio (SXM or AM/FM) audio is to increase the head unit phone volume. Unfortunately, since the head unit doesn't have a cell radio built in as a cell phone would, the volume controls for the phone audio stream aren't shown (at least that I could find when I dug down into the android settings in the developer menu).
Note this isn't the same audio stream that you use when you make a call -- that is the bluetooth phone audio stream. So increasing the volume there when you make a call won't help.
However there are a lot of volume control apps available. I grabbed Volume Control Widget by Serkun, used the OneClickInstall to put it on the head unit, opened it on the Pilot, bumped up the "voice call" volume (15 seems good to me, but it will go up very high if that is what you want), started the radio, and then started Waze. Waze volume now sounds great.
Note that you need to have "Play From Phone Speaker" turned on under Waze Advanced Settings for this to work.
Once you set the volume, it will stay at that level until you change it again in your Volume Control app. Waze doesn't reset it, nor does it revert back to low when you turn off the vehicle. I haven't tried it, but I suspect that you could even uninstall the Volume Control app after you set it where you like if you don't feel the need to adjust it occasionally. Assuming you do not uninstall it - still a little bit of a hassle if you want to change the volume in the middle of a drive, you have to go back to the home screen, open the Volume Control app, change it, and then go back to Waze, but personally I think I'll be good leaving it at one setting the majority of the time.
The GMaps version that I have installed on my phone has a similar "Play over phone speaker" setting so I believe it is possible to do something similar with it. However, that setting isn't showing up on my Pilot. I may try to dig into that some, but I've been pretty happy with Waze so not a high priority.