The uploader is not making "incorrect assumptions" about the data. It is looking at the data density of the images which is how many megabytes are present to represent how many pixels. If this number is below a certain threshold it is deemed to be of low quality. Low quality images are prone to fail in our system since the details of the images are no longer reliably transmitted to the system since they have been replaced by compression approximations.
The changes compression makes to the human eye can be small but those changes make a big impact to the performance of our system's feature detection algorithms.
If you have figured out a way for it to work, great! There are automated messages to let users know that other software has touched the images/tags. We don't stop you from uploading them but we let you know about it.
If you are having issues with the auto white balance why not try just setting it to sunny or cloudy so it doesn't change mid flight? The color is always going to change if the lighting conditions are variable.
We do not in any way prohibit doing color corrections. We just let users know that the source image tags may have been altered since this happens frequently.