Please be advised: this entry is incomplete.
Origin unknown.
There are a couple of variations on this. In one, Y is really the short form of X, e.g., in “when I say ‘rare’ what I really mean is that it was thought to be extinct until 1994 when a hiker found a grove of about 100 of the plants in the middle of a one million acre wilderness area outside Sydney, Australia.” (link) In the other, Y is the opposite of X, or they contrast in meaning in some way. E.g., “when I say ‘today’, I mean ‘tomorrow’.” (link)
The Snowclones Database 
A common variant of this is “And by X, I mean Y”, where X and Y are usually quite distinct things, with the contrast intended as humorous. X and Y as opposites is not required; often, they’re merely unrelated. Currently, “And by * I mean” gets around 760,000 hits on Google.
This one has been around at least since 1749.
Cf. Thwackum in _Tom Jones_, Bk. III, Ch. 3:
“When I mention religion, I mean the Christian religion; and not only the Christian religion, but the Protestant religion; and not only the Protestant religion, but the Church of England.”
“I’m going to go finish my work, and by ‘finish’ I mean ‘eat’, and by “my work” I mean ‘some more chips’.
Monty Python:
“There is NO cannibalism in the British Navy. And by that I mean there is a certain amount.”
From the great animated series “Clone High”:
(teenaged clone of) JFK: “Hey, let’s all go swimming in my pool, and by pool I mean bathtub, and by swimming, I mean sex.”