surely we can also assume that the system has safeguards in place to either stop a transport of a lifeform without transporter adjustment, or automatically "up the bit rate" of the transporter mode to make it safe for travel.
We don't generally have a reason to believe in the transporter being an actively safe device. It beamed the two guards into vacuum in "And the Children Shall Lead", did not ask for permission or leave a log about the split/duplicate thing in "The Enemy Within", and failed to inform anybody of van Gelder being in one of the boxes in "Dagger of the Mind", or of the Salt Vampire beaming aboard in "Man Trap" or the Scalosians in "Wink of an Eye". So there are plenty of examples of both lack of alert and lack of independent protective action.
In theory, the device being able/allowed to select its mode of operation sounds nice. But in practice, there are too many instances of our heroes having no real idea of what is really being transported. The device knowing and not telling is not particularly plausible.
The idea of neural patterns being different from other patterns is an unfortunate one, but I guess we have to accept Rom's technobabble from "Our Man Bashir" one way or another. Then again, we could say Rom is mainly discussing the fundamental differences between how transporters work and how holodecks (and, possibly, their associated replicators, which might be the devices safekeeping the bodies of the victims) work.
What do we make of Odo's initial statement?
Odo: "This is more complicated than just an ordinary transporter pattern. We're going to have to preserve all the neural signatures of everyone on that runabout. Do you know how much memory it would take to save just one person's neural signature, much less five? "
Why would this be more complicated than an ordinary transporter pattern? It's just five people in the pattern buffer, isn't it? What could be more ordinary than that?
By far the most problematic idea here is Odo and Eddigton's (informed, at least in the latter case) insistence that transporter patterns are data that can be stored on a computer. But perhaps only those neural patterns are data, and the rest is phased matter? Or even, perhaps data is only involved in keeping the five neural patterns intact and/or separated from each other, as the original accident might otherwise result in them getting scrambled?