There really aren't many functional differences as such. These are just design solutions to achieve the required aerodynamic states.
Considering LEVCONS are part of the PAKFA, IMHO, the radar returns may be lesser than Canards. Perhaps the aerodynamic qualities of Canards are greater at low altitudes as compared to LEVCONS. N-LCA uses them for primarily landing while PAKFA probably uses them for an entirely different purpose.
The few reasons why Canards impart a higher RCS, from what I can see is,
a) Canards are in not the same plane as the main wing (JAS-39, Rafale, Typhoon) and hence provide an additional edge for radar reflections.
Furthermore most canards designs (as in the euro birds) are not optimised for planform alignment. with the exception of YF-23 naval variant which had proper planform alignment.
A LEVCON on the other hand can be both edge aligned as well as planform aligned.
b) Any moving surface in the front aspect will have a seam, a gap with the adjacent surface, and any surface imperfection will bounce back em waves. A canard will have the widest seam considering the degree of movement and the bending forces it will experience. A levcon might be able to get away (strictly in my opinion only) with lower a smaller surface gap and your regular leading edge managing the highest tolerance in finish. A conventionally designed fighter has the option of hiding the seams of its moving surfaces behind the main wing, while a canard does not give you that option.
Just my 2 cents.