An external booth replacing the conventional water closet, or a cybernetic implant personal substitute bowel?
External is just a matter of choice.
Internal however would bring up all that Eugenics hoo-har about man vs. superman, not to mention if every human being was carrying a significant and standardized powersource inside them, the baddies might think to use it as a marker to target their weapons with...
And how long is this power source supposed to last?
A dilithium reactor an inch away from your reproductive plumbing can't be good for the species or planned parenting.
If the powersource for the transporter is supposed to last a hundred years, then our bunghole is going to compensate, so that after two decades, if the transporter breaks down, people are going to die.
The same problem mostly for a shorter term battery that needs to be replaced every month. You see how well women do with the pill. Replace your battery or die. Gods forbid any one monopolized the supply of batteries that they couldn't leverage the Federation for anything they felt like.
Then of course you got kids playing with this hardware to create birth control and abortions, and then they fuck up and transport a lung outside their body when they miss the three month old foetus they were aiming at, they don't want to tell their parents about.
The Drone "One" had internal transporters.
If you can transport waste, the tech to transport yourself can't be altogether too different
Which brings us to the Prime Directive Issue.
Any Bullshit little aliens running around still burning plutonium to make their starships run, is going to think it's Christmas that the secret to transporter technology is in not only inside every human being, but the also inside the weakest and stupidest human beings too, that numerous Federation Citizens are going to be waking up in bathtubs full of ice with their lower intestines removed.
So these devices would have to come with self destruct switches to ward against espionage, which would equate to kill-switches since these humans suddenly can't shit.
So again, you've got bad guys tapping the killswitches or transporting one persons organs inside another persons skull to begin an invasion with gusto exploiting human stupidity to do such a woeful and lazy thing to themselves.
Totally Talos IV