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.
Precisely correct. Even under the circumstances Kirk was facing at the time he took back the Enterprise
, there was no reason for him to beam directly onto the bridge just so he could get back aboard the ship. Given the state the Enterprise
was in at the time he boarded the vessel, there's no way of knowing what he might have beamed into. The bridge was a mess, as was the entire engineering section. Why risk causing a major disruption by emerging right in the middle of a work area?