Tyrphanax said:

Having grown up with the SEs, I had never heard that line until I started getting into preservations. When I heard it, I immediately loved it and wondered why they'd ever take it out of the film.

I'm pretty sure it may have already been a variant among certain pre-SE versions of Empire. Perhaps from the 70mm? Others here know far better than me. From what I've read, that alternative line was used simply because it was deemed to be of higher quality than the other, and that the nobody even realized it was completely different from the one in the original film until after it was released and fans noticed it. A perfect example of how much love and care these films have received over the years.

Apparently, the line heard in the SE is straight from the script, and the one in the theatrical Mark Hamil came up with himself (much like Harrison Ford's "I know"), and they liked it so they used it.