Ha!
If I were only going to make a print PDF, I might keep \flushbottom,
because it does look nicer.
But I think matching is more important.
There is still a slight discrepancy between colour and print PDF: after
each exercise section, \clearpage gets interpreted in 2-side layout as
\cleardoublepage, so that each chapter and section begins on an odd
page. Those blank pages are left out of the 1-side layout.
So page numbering is a bit different, but each corresponding page will
match up.