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 Are we meant to interpret this as La’an digging through the regulations for an outdated excuse to be present for Kirk’s arrival, or is this a legitimate precaution that we should expect is routinely taken quietly and off-screen?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?
When she and the alternate Kirk went on their little time travel adventure, the episode ended with La’an calling Kirk to ask about some kind of bullshit info she needed for Sam Kirk’s file.
I saw the whole security excuse as an extension of that.