When Kirk comes aboard the Enterprise at the beginning of the episode, La’an is in the transporter room to receive him. Her actual motives for being there are… complicated, but she claims to be there so she “can run a security clearance on [Kirk].” Allegedly this is “just standard operating procedure”, which Commander Chin-Riley does not question.
To the best of my knowledge, we’ve never seen a security officer carry out this “standard operating procedure” before, nor do we actually see it done here. further, Kirk is a reasonably respected Starfleet officer who has been on the Enterprise before (and quite recently). It seems unlikely that he represents a reasonable security risk. Are we meant to interpret this as La’an digging through the regulations for an outdated excuse to be present for Kirk’s arrival, or is this a legitimate precaution that we should expect is routinely taken quietly and off-screen? If the later, what could actually be going on that requires the physical presence of the security clearance and can’t be accomplished by a simple scan?
Well she was obviously making an excuse to be there and everyone in the room knew it. Id guess the security clearance was something like manually verifying his identity and registering him with the computer as part of the command staff. This would normally be the sort of boring paperwork the computer or a lower level security person does off screen, but she wanted an excuse to be there and the clearance was technically something she was responsible for.