From what I understand, they are meant to actually just be squeezed (and formed to the inside of the frame in whatever grooves there are, or better yet, use a rototool or hacksaw and cut a notch the size of the flat part of the cable so the door closes flat on the cable) in between where the frame and the door meet when closed, but this doesn't seem like a good idea, things like wear and tear from opening and closing the door, and not being able to close the door completely, etc would come into play.
I suppose one could remove [*] and run it under the threshold/track below (or even one of the sides) the sliding glass door, then _carefully_ replacing the track and threshold over the flat part of the cable afterwards, this would probably be best under a part of the threshold where noone is likely to step, so as not to have the threshhold cut into the flat cable below from someone standing/walking on the track/threshold during normal use.
[*]: Depending on the design, you may have to lift up and pull out one or both of the sliding glass doors to get to the screws for the threshold and to pull up the bottom track, so doing it under the threshold, instead of from one of the sides will be more work (and danger).