AFS and Trutrak aren't competitors. Trutrak is the OEM supplier of the APs that AFS sells. It is a very tight and complimentary relationship. Also, when was the last time you ever paid list price for something? Resellers sell both products at a discount.
The differences if your have an AFS EFIS is that you'll have a few more button pushes on the AP if you use the genric TruTrak model. There are also some differences in how the AP will function if the EFIS should fail. None of these are major differences.
If you are planning on an AFS EFIS, just get the AFS AP and build on.
bob