You don't seem to understand how entity_set_size works:
Its runs this: pfnSetAbsBox
That is the controller of the main bounding box, so running jumping or w/e this is constantly updating.
How it works:
It gets the origin of any given entity then adds on the mins & maxes values.
So using this native you need origin + min and origin + max, else it won't work as you expected. Its how I was able to make my tripmine script on AMX forums, so that you could stand on them instead of bouncing around like a tit (original)