In my opinion, whatever you use should be put beneath whatever it is you are going to seal, not on top or on the edge. In other words, for a window, the sealant goes beneath the flange, before you install it. Prep both surfaces properly, of course.
A "top it off" bead does not do anything for the seal (if it did, all those windows
that people try to re-seal by just putting a bead on top would never leak again - and we know how well that works), but does create a dirt trap.
I like the butyl tape (superior to the non-butyl tape), but there are other decent sealants (just not silicone!).