Drama and progress
One way to interpret the title would be that the hypothetical, fictitious success of Babbage's Engine yields a Difference that could be measured. This shows a dramatic irony between progress and change. Namely, the novel shows that one small detail might have radically changed the course of history forever. If one machine had operated better than expected, perhaps history might have unfolded the way this novel describes, instead of the Industrial Revolution and the Technological Revolution happening independently.
History and irony
The past seems set in stone and fixed, but this novel makes ironic usage of history. Through the creative decision to place computer technology further back in history, a measure of the change can be seen. This is ironic because to a modern reader, perhaps computers and technologies seem obvious and self-explanatory, but they are not regarded that way in this historical fiction. The ironic use of history shows the reader an objective measure of progress.
Regime change
One consequence that comes up in this novel that does not seem obvious at first is the regime change from an old way of life into a new, chaotic way of life. This means an end of monarchy in Britain and the rise of technocrats and new ways of power. This is ironic to the characters in the story because the change was started by a simple machine (kind of like Eli Whitney's machines). The effect of this is ultimate because it brings drastic changes in the nation's economy.
Climate change and irony
The characters of the novel start complaining about a "a great Stink," which is supposed to be a parallel to the London Smog of 1952. Basically, because of the accelerated changes that the Difference Engine brings to Britain, the realities of climate change and pollution are pushed back even further in time. The dramatic irony of this is that in the modern age, science has progressed to the point that we understand the influence of technological progress and climate change. The reader will likely see the "Stink" as a reference to the problems of pollution and climate change.
Power and adaptation
Sybil is a living embodiment of an ironic reality that faces the whole nation of Britain in the book. For instance, Sybil's father believes a standard, traditional opinion about power, but that makes his point of view too rigid, and he is removed from his seat of power. Sybil, on the other hand, sees what was veiled from her father by dramatic irony: she sees that one must be adaptive and willing to change in order to gain or preserve power. Since he is not willing to adjust, he fails, and Sybil's power comes from her flexibility and not her persistence.