The large transparent image is just what I do at the moment.
It is centered, so the X is always at image.width/2.
The game engine I am working with is Adventure Game Studio, and it does not support the atlas.
Also, to keep things compatible for every kind of engine, I try to stick to only image files, so the animations can be used by everyone.
As an artist and animator, I am planning on selling some animated characters (did them with Skeleton 1.1 before, a very old tool you may know), and I think, simple png files are best for that purpose.
My combined workaround at the moment:
The large transparent image stores the offset, then I duplicate all the frames and batch flip them with Image Magick, afterwards I crop them with SmartCropper and then delete the flipped ones.
That is quite slow, but it works.