Just because Scotty can figure out transwarp beaming in the prime timeline, and future Spock knows it and does it in the nu-timeline, that doesn't mean that anybody else can figure it out in the nu-timeline.
But on the other hand, you gotta expect that someone who knows that Kirk was jettisoned to Delta Vega is going to blab to the wrong ears about how he was beamed back aboard the ship. Maybe Starfleet Security spoke to the Enterprise crew and impressed upon them their duty to keep their lips zipped.
And Genesis in planet forbidden.
My problem with any long distance beaming is that it flies in the face of established Trek Tech i.e. that you need to generate and maintain a beam of energy (presumably transmitted through subspace) to keep the pattern intact. Communications signals can be sent about 27 light years but can you imagine the amount of power it would take to send a transporter pattern over much longer distances - you need more powerful transmitters, more energy. Using a decrepit shuttle and an algorithm with no modifications and no consequences was poor storytelling IMO. The energy needed to maintain the pattern seems to me to be the limiting factor that was brushed under the carpet. I have no issues with how they dealt with transwarp beaming, only the distances involved.
I get equally nervous about antimatter bombs. You would have to beam a functional magnetic field to prevent the device exploding when the matter container and anti-matter inside it get dissolved and combined in the beam. Having said that it's no more of a problem than the kill and copy issue relating to living matter.
It's explainable if the matter and antimatter is simply phased (my preferred interpretation) and only quantum-linked energy forms the energy within the confinement beam.