Most things you can do to change a GPS receiver are harmless. The ones that might matter that I can think of are changing whether you cold start and making sentences come in less frequently or not at all (for receivers that support configuring what and when you get sentences)

You could simply filter all proprietary sentences but some of them are useful. Making a "blacklist" would work but could get messy, since it means we need to know what every proprietary sentence *is*.