I hate those explanations. I can understand Symon Pegg just ignoring the issue for Beyond, and it works fine considering the setting, but I think tackling the implications of transwarp beaming is really something which needs to be done.
WHAT implications? It's a stupefyingly dangerous way to travel that requires a fantastic amount of intelligence and precision to perform and even then you have a very high probability of dying a horrible and humiliating death wherever you materialize. The only people likely to use it are either crazy or desperate or some unseemly combination of both.
Its advantages are as overwhelming and obvious as are its dangers, but hiding it does no good especially if another civilizations gets it and does use it.
I actually don't think it's that big a deal. It's difficult to use and not all that reliable, so it's not something a CIVILIZATION would really adopt as a practical means of transportation. A few crazy individuals and/or daredevils, sure. Section 31 probably has a network of these things setup for quick escapes, as do probably the Tal Shiar and the obsidian order, but the difficulty of using them is their own limitation. In that sense, it's probably like
the whole skyhook thing the Navy dreamed up in the 60s.
Besides, weakness can be written into it with ease, such as not working through shields, and only being able to beam to planets and systems which have been carefully mapped.
They already did that, remember? Scotty beaming into a water tank and nearly being sliced to pieces is pretty much the definition of "weakness." You beam blind into a location you can't see, you have NO IDEA where you're going to land. Consider, for example, that 70% of the Earth's surface is covered with water, which means blind transwarp beaming from a location outside of Sol gives you barely a one in three chance of even materializing on land, let alone in a safe landing site (e.g. not inside of a tree trunk or on the side of a very tall mountain or in the middle of a desert or in the middle of the freeway).
It's not really even a new technology, it's just a novel way of using transporters that we rarely see because it's really REALLY dangerous. I'm sure there are a dozen of those little tricks floating around and I'm sure the reason we never see them is because there's only a handful of people in the galaxy crazy enough (and/or smart enough) to attempt it.
The classic example of this is Spock's "breakway time warp" equation. There are dozens of ways to time travel, but Spock's method is by far the easiest. So how come there was no fan consternation about the implications of THAT technique? What would prevent, say, the klingons or the Romulans from traveling back in time to destroy the Federation before it started? That's simple: Spock is the only one smart enough to run those equations and the only one stupid enough to try it on purpose.
It also means ships are still important for exploring the periphery and projecting power.
Starfleet doesn't project power.