The key will be that the prohibition remains in place holus-bolus across the country, in section 35.
The guidelines you're talking about will say, “Buddy, if you're planning to build a stream crossing in this case, and you follow these standards, it's extremely likely that you will not violate the prohibition, because you will not cause serious harm, and so on.”
However, if we got to a scenario in which Buddy says he's planning to do that, and it happens, and his neighbours rat him out or something, saying that's not what he actually did, the department will be able to go in. In that case, he will not have an authorization that we would be enforcing; instead, what we'd be doing is saying, “You told the community you were going to behave in such a way that you would not violate the standards and guidelines, but in fact we have...”.
In a scenario such as that, the department would still have the authority to go in and lay a charge with respect to violation of section 35, rather than of the authorization terms, because he wouldn't have them.