It seems that GTK+ 3 and Qt 5 are being adapted more to what is known as "touch screens" and so scrolling using "touch pads" is always smooth, with both of these toolkits, even in cases where smooth scrolling is not enabled.
Once smooth scrolling with typical mouse is disabled, disable any other smooth scrolling (e.g. touch pad, touch screen etc.).
P.S. GTK+ 2 and Qt 4 do not smooth scroll on touch pad input, once smooth scroll is disabled, and sometimes even by default.
You might want to test Qupzilla (Qt4) against Qupzilla (Qt5).
Close this ticket in favor of https://sourceforge.net/p/qt5ct/tickets/17/