Ugh. Didn't you get enough technobabble to explain away dramatic conveniences in Voyager?
Making transporters require a beacon is something that could easily be written into the future of the franchise and it would make more sense.
Also, transporters requiring a beacon adds lots of potential for drama. You have to board a ship or land on the surface to rescue the person. A comm badge can be removed to lose the homing signal. How is it that they can know who they are locking onto and beam them up when they don't have any beacons on them and are out of sight? Even a throwaway line about all Starfleet crew having a beacon embedded in their skin would be nice. Then you can have an episode where someone digs it out and connects it to a communicator or something to boost the signal.
Having inconsistent transporter use actually removes drama because you never know when they'll decide it's now possible to transport someone/something. Having set rules forces creative stories to deal with situations where a transporter beacon isn't available and allows for cool scenes like the S3 Enterprise episode with the pirates.