We don't know if Maltz controlled the transporter from the Klingon bridge.
We have to consider that Kruge apparently cast the fate of his boarding party on the mercy of the transporter of the
Enterprise. The Klingons materialize in the blue haze of the Starfleet transporter (not the red Klingon one), on a Starfleet transporter pad (rather than directly on Kirk's bridge), after Kirk has said that he's doing the energizing, and Kruge has told his own crew that he wants (his own?) transporter to stand by.
Why would Kruge agree to Kirk being in charge here? The natural assumption would be that his own transporter would be broken down or at least unreliable after Kirk's torpedo attack. Probably not completely non-operational, because Kruge originally orders his boarding party to the Klingon transporter room, which wouldn't be necessary if Kirk's transporter room were doing all the work. Plus Kruge says that bit about transporter standing by - looks like there was a change of plans when a less suicidal alternative for moving from ship to ship manifested itself.
If the above speculation holds, then it would make sense that the Klingon transporter would be under close supervision (and perhaps indeed ongoing repair) when Kirk and friends beam up. It would be odd for Maltz to be operating the system on remote.
(Of course, it may simply be that the Klingon transporter was used in boarding Kirk's ship, but that something in the basic nature of transporting made the Klingons materialize in the middle of blue rather than red VFX... There's fairly little other evidence on how these things work, besides ST3. We do have DS9 "Dramatis Personae" where a Klingon transporter initiates transport and tries to materialize the transportee in red effects, but this fails and our heroes finish the transport with their own Cardassian hardware, in the amber Cardassian effects. So color change is possible, but seems to be related to handing over control of the process; Kruge either didn't do the transporting at all, or then handed over control to Kirk, both options calling for an explanation. And knowing Klingon psyche, only a force majeure like equipment failure sounds believable.)
Timo Saloniemi