I'd like to make an export setting for this, but probably won't get to it for a while. 🙁 As a workaround, you can use a large transparent image to cause the image frames that are exported to all be the same size. The image needs to be as large or larger than any of the animations, in each direction (or at least the left and top or bottom sides, depending on if you use y-up or y-down at runtime). Since you are trimming whitespace this won't add any size to your images. Once all your frames are the same size, the 0,0 position in Spine (the axis lines) will be the same in every exported image and you then know where to draw at runtime. Make sense?
Here's an (extreme) example: create a transparent image that is 1000x1000. Place it so the upper right corner is at 0,0 in Spine. Now all your exported animation frame images will be at least 1000x1000 (probably more since your character is likely above and to the right of 0,0). In each frame image, you know that 1000 pixels from the bottom and 1000 pixels from the left corresponds to 0,0 in Spine, which is your reference point for positioning at runtime. Eg, if you want to put your character at 200,300 then draw the images at 200-1000,300-1000 = -800,-700.