There are two distinct items being discussed here. And this is my opinion.
First, positioning flights. These are where your employer is sending you from airport 1 to airport 2 so you can then be crew from airport 2. This is considered work and counts towards whatever hours, charges etc you have. You should be listed on the manifest as crew or a passenger for this. If as crew, then crew routes are open to you. If as a passenger, you should have a ticket and boarding card and use the passenger routes regardless of the fact that you may have a security pass for airport A.
Second is commuting. This is where you choose to live near airport A but are based at airport B and it is your responsibility to get to airport B. In this case, this is not work and you should always be on the manifest as a passenger with a ticket/boarding card. You should ALWAYS use the passenger routes in this instance.