How is transubstantiation different to annihilationism? The end products look the same

Well, from the observer's perspective the results of all three processes look the same, because according to the Aristotelian models of sensation and perception that fit with these explanations it is only the accidents that human beings are capable of percieving - we don't have the capacity to detect substantial forms qua substantial forms.

But you're pretty much right. Transubstantiation is about swapping over the substance but leaving the same accidents in situ (and is thus a form of local motion in Aristotelian terms, albeit one Aristotle himself didn't think possible) while annihilationism is about getting rid of both substance and accidents and replacing the whole lot with a completely new set of substance and accidents entirely. In the first case you end up with substance B under accidents A, in the second case you have substance B under accidents B. Accidents B may look exactly the same as accidents A, but they aren't. Numerically accidents B are a separate thing, in the same way the colour red in two red apples may be the same colour, but the "redness" of the first apple is supposed to be a different instantiation of redness from the redness of the second apple.

Which, inevitably, led some theologians to wondering what exactly happens to the substances and accidents that had been displaced. Did they just hang in the air somehow? Did they just cease to be? Did the ascended body of christ in heaven somehow acquire the substance of the bread temporarily? Did they return to the bread and wine eventually (generally before excretion - people really didn't want you crapping out bits of christ later in the day, that would be theologically very unseemly).