^The line also sets up the fatal transporter malfunction that occurs shortly after. The problem is, even if this is what the intent of the line is, we are left with the problem that everything we know about transporter technology as of that film suggests that Enterprise's transporters not working shouldn't prevent Kirk from beaming aboard. Starfleet must have a few dozen working transporters at least, and even if for some reason the ground transporters couldn't beam him up to a ship, the transporter room on the Orbital Complex certainly should.
Sure, they could
beam someone directly to the ship without going through its own transporter, just have them materialize on the bridge or somewhere, but that doesn't mean they would
. After all, there's such a thing as naval protocol. You just don't barge onto somebody's ship, even your own (or even a barge, I expect), without getting formal permission to come aboard. Had it been genuinely urgent for Kirk to get to the bridge that minute
, then sure, they would've waived protocol and beamed him up there from HQ. But as it was, Kirk opted to follow proper protocol and come aboard at one of the accepted, approved entry points. Failing the transporter room, that meant a docking port.
Another thing to consider is that while TOS did show people beaming to other ships' corridors and bridges in episodes like "The Doomsday Machine" and "The Tholian Web," other episodes often showed that it was preferable to beam from pad to pad when a receiving pad was available. And "Day of the Dove" (I think) presented intraship beaming as hazardous due to the risk of accidentally beaming into a bulkhead or something. Maybe all the metal and plasma conduits and stuff in the way creates interference that can disrupt the transporter beam, so it's better to beam to a pad if one's available. It may have been at least slightly safer for Kirk to beam to the office complex and take a short travel pod ride than it would've been to beam directly aboard without the benefit of an active receiving pad. Particularly with the fluctuating energies and interference patterns of a ship undergoing the final stages of its refit and activation.