But...

“As soon as their shields get low enough to do a 10% accurate transport, transport as much of their warp core from engineering to the bridge as you can. Then when shields fail entirely, get the rest.”

Though maybe the core shielding would also block transports, or else you’d figure “eject warp core” would involve the transporter. Or maybe they could even just use “stick the warp core in the transporter buffer until, uh, we delete it? Or use a simulated copy to figure out what transformations we could apply to fix it?”

Or: “Just run the transporter over their ship and move random molecules around.”

Or, depending on exactly how transporters work: “Convert as much of their warp core shielding into plutonium as you can, such that we can still warp away from the blast in time.”

If you could just transform matter, it could be possible to use a transporter and a pattern to have a shuttle sneak into an area and build a fleet of warships. Or to build one if attacked. I think been the replicator and transporter, Star Trek has the tech covered, it’s just a question of energy, but I have a feeling that the amount of energy needed to create Starships (minus warp capability) is trivial compared to the amount of energy required to create and sustain a high factor warp field.