I'm able to animate my collision polygons, and they (somewhat) work, but I've found that sometimes the polys are in the original place/shape despite being switched via script AND the polygon shapes are showing up as the animated version that I want when "Visible Collision Shapes" is checked. I think that this is a bug. (I'm still using Godot 2.15, BTW).
I also made sure to have the actual coordinate position set at exactly x 0, y 0 and only have my frames change the actual polygon point positions. Maybe there's a loop I've created where the Area 2d that is sending my collision signals is being bypassed -- hence why they work some of the time. My game will not work without animated polygons, so I'm stuck until I find a solution. (Hopefully I won't end up having to (re)learn C++ and fixing then compiling the durn engine from scratch, and it's just something I've overlooked or there's a workaround for it.)