Here you go. I found the solution somewhere online and decided to make a video to help others out. Now when I get iMessage or any other alert like when Siri talks or a Waze direction plays, the volume is much more usable and less terrifying!
How to adjust volume of Apple CarPlay and other alerts in Toyota infotainment. - YouTube
How to adjust volume of Apple CarPlay and other alerts in Toyota infotainment. - YouTube