If you opt to use the existing factory racks there area couple of
things you can do to help offset the limitations.

A lot of factory racks really are little more than flimsy
ornamentation, at least as far as cartopping a boat.

For starters do not tie off to the rack alone. If something fails at
highway speed it is likely to be the rack, so having the boat tied only
to the rack is nearly useless. At the very least tie off the bow and
stern to the vehicle. Ideally even the bellylines across the hull would
be tied off to the vehicle as well, but that sometimes involves straps
through the car or S-hooks marring the paint job on the quarterpanels.

If the crossbars are particularly flimsy/flexible, especially if the
weight of a boat tends to bow them downward it'll help to stiffen
them up by stuffing a piece of foam between the rack crossbar and the
roof (those foam gunwale blocks that are sometimes used carrying canoes
on car roofs may work, or just a chunk of minicel carved to shape).

If the factory rack crossbars are so narrow that the gunwales of a
canoe nearly span the crossbar width I'd recommend rigging up some
kind of gunwale chalks; something on the outside edges of the crossbar
to help prevent the canoe from slipping off sideways. It'll also help
if you use two bow and two stern lines, so that these lines go in a V
from the stems of the boat down and out to the edges of the vehicle
bumper or tow rings or whatever you can find to tie off to (again,
having some sturdy S-hooks available may be handy).