The manual is very specific on what is allowed and what's not. If the tech isn't a prick he'll look the other way but he can fail the car for even simple things like non-stock hoses on the PCV and idle speed system. Very few will look the other way for a missing main cat, EGR, evap cannister, things like that. It takes a lot of money, time, and experience to obtain emissions certification (I know, I went through it) so most techs aren't going to risk it beyond a small point. Not to mention the fines they and their employer can suffer. They know the state is constantly running undercover stings to find them.
Beyond the visual and running the car on the machine the tech is out of the loop. It's all done automatically and the results transmitted to the DMV then and there. About the only way to fudge the emissions test itself is to get the tech to sniff a different car than the one due for the test and very few will. From where I sit those that do should be fined and have their licenses yanked. I also have little sympathy for people who screw with these engines without knowing what they're doing. So many failed emissions (and continue to fail) the car ended up on the Test Only list. Now everyone has to deal with that hassle. Just another example of how a small group of idiots screw things up for everybody.