Indeed, it's more or less directly contradicted by "Datalore", even if only in retrospect.
That is, Lore goes to a cargo bay equipped with a cargo transporter, with the make-believe intent of "initializing transport" from there, but with the real goal of merely getting the shields down so that the Crystalline Entity can attack. He has zero motivation to readjust the settings of that transporter at any point. At the climax, Data throws him into the transporter, and Wesley activates the transporter with a simple keypress, again with zero motivation of making the system android-friendly.
Now, at the putative "molecular resolution", this should kill Lore, as we know the Soongian androids are sensitive to pretty much the same things humans are. Yet we later learn (probably against original writer intent) that Lore survives - forcing us to believe not only that the cargo transporter default setting was android-friendly, but also that Wesley dropped the shields (perhaps unwittingly, as Lore supposedly had rigged the console to do that - what else would he have been doing fiddling with the controls, when he clearly had no intention of beaming out a tree as he had claimed he'd do?).
Another interesting datapoint: in "Peak Performance" it appears that Wesley smuggles antimatter into the transporting process, since the Hathaway
is originally said to be crippled specifically because of lack of antimatter whereas Wesley's trick somehow uncripples her. The transporter operator does not know of the presence of the antimatter, so he cannot be using any special trick to enable its safe transport. So, personnel transporters can move antimatter by default...
Various TNG and DS9 episodes dealing with cargo transport mention substances that are sensitive to transport and indeed require special settings or modern (as opposed to outdated) transporter models. This suggests that transporting of cargo is every bit as demanding as transporting of personnel, and probably more so. The idea of "molecular resolution" is further undermined, then. Who knows what precious cargo would be lost if the resolution was wantonly dialed down from humanoid-friendly levels in "Dagger of the Mind"?