Yes. I never visit the counter when renting from Alamo at MCO, and I routinely use VTP. Even before VTP, I never visited the counter at MCO and just used my own EZPass-compatible transponder, entering the rental license plate information on the transponder web site.
You refuse the toll program in either your profile or during online check in. I don't use Alamo but have with their corporate overlords. Enterprise and National, it's in your profile as a preference so it's already denied.
Also, the default is opted out, you have to opt in to be included.