At 1800's time, was there so much knowledge about music theory, or they were human prodigies? (liszt,chopin)
I'd suggest they were both humans
and prodigies. At least in many cases!

I don't have a definitive citation, but it seems almost certain to me that, especially among prolific, accomplished improvisers as was the tradition for quite a long time, your average early-to-mid 19th C composer-pianist had a more intimate knowledge of common-practice major/minor (and beyond) music theory than perhaps is typical today.
As well as many more hours of executing all kinds of relatively sophisticated voicings in cadences, and facility with modulating in whatever complicated (or not) fashion he or she would have chosen. In addition to their own favorite manœuvres at the keyboard, perhaps to distinguish themselves from "the masses."
It was a great age for experimentation, as you know, so it wouldn't surprise me. I would bet, prodigies or not, they worked very hard at exploring possibilities of interest to them.