I've tried using things like swapping the up axis when exporting to dae or fbx and those made no difference sometimes.
Right now though I'm not exporting geometry. I'm writing a script that exports the names of objects and their transforms and bounding boxes. I currently don't have a level editor so this is the easiest way for me to make environments.
I have various hacky ideas for how to do it that I've used back in the day but I thought I'd learn how to do it right once and for all, if there's a way.