I have read/heard the same thing about bondo vs. fiberglass. Since both use the same activator, I would think the resin isn't the part that is susceptible to water, but the other primary material might be the issue. And now searching (via Google), it looks like the other primary ingredient in body filler is clay/talc which absorbs water, whereas fiberglass does not. So, that is the difference.
In applications for which I can not be 100% sure that exposure to water is eliminated, I use fiberglass filler. For example, I used a bit in the inside of the dog leg of the quarter panel/rear of the rocker, in an earlier repair, mainly to fill pitting and a few very small holes left after sandblasting prior rust damage. I will attempt to seal the car so water will not get in there ever again, but I used a bit of fiberglass filler there just in case. For repair areas where I am sure water will not ever be present, I use standard body filler. Along that door edge, seam sealer will seal the lap joint of the skin to the frame, primer and paint will seal the outside of the repair, and I will be using a spray on sound deadening coating on the entire interior of the door which will seal the joint on the inside and keep any water away from the area.