You are correct in your conclusion, but not regarding the standard procedure being a 2-pass survey. The standard is a single pass unless enough trout are collected to suggest that the stream may be a viable Class A candidate. If so, then multiple passes are done and the survey may need to be expanded to multiple sites in order to meet certain standards for Class A streams, such as at least 10% of the Class A section having been sampled. On such occasions, we in the SE do a three pass survey or a 2 pass Petersen. The Petersen requires a return trip, but that is ok if there are multiple sites being sampled.
Forgot to answer your original question: yes, the universities, etc are supposed to follow standard PFBC procedures with respect to single pass surveys. Some add additional work to that because of their own interest. My understanding is that these contractors do not have to do population estimates, but are to let PFBC biologists know when a potential class A population has been found. Then PFBC biologists do the "Class A survey," which involves a different protocol and more intense sampling.