I think I have some experience which may help answer this question (despite applying to a different field). I decided late last year that I was going to take a leave of absence to conduct research. This decision came after I had already applied through VSAS and directly through schools themselves. I was re-accepted into both programs I got into last year (1 through VSAS, and 1 using its own system).
So in my particular experience, I don't believe that turning down an elective medical student externship is necessarily frowned upon by program coordinators (and I wouldn't think many other people in the department aside from the program coordinator have knowledge of who turned down elective spots).
Furthermore, I applied to more than 10 programs last year and was accepted into most all of them, so this year I applied to far fewer places knowing that I'd likely get the spots I wanted (though some programs seem to fill up very early on so I knew to apply to those even earlier this time around).
Hope that helps.
