Sorry but as non native english speaker and hobby coder i couldn't get much solution out of the documentation and you kinda just repeated the documentation...
sooo i played around a bit with those two functions and at the end its quite simple :D
fHTML::encode('<p>la*;l"a%</p>')
will return
#!text/html
<p>la*;l"a%</p>
and at your website it will look like this:
#!text/html
<p>la*;l"a%</p>
fHTML::prepare('<p>la*;l"a%</p>')
however will return
#!text/html
<p>la*;l"a%</p>
you will see:
#!text/html
la*;l"a%