That is often the case. I think its always favourable to be light on the image pre-processing.

The image can be captured and saved quicker. This allows more shots per minute and saves battery power. Also when you snap the picture you want it saved NOW so you can instantly take another, not a few seconds later. So processing will always be primitive (meaning less precise and lower quality) compared to what you can do in GIMP, Photoshop, etc, where it doesn't matter if it takes 30 seconds or minutes to process.

Also its far better being able to undo if the processing makes the image look worse, so doing as little processing as possible is ideal. In many cases you might take an excellent photo but the mandatory processing will actually cause a poor result. This is why professional cameras do RAW mode with no processing whatsoever.

That said, as we are dealing with Linux here I would expect third-party software to offer less or no processing, whereas the stock software to be a "happy medium" trying to get the best perceived quality the majority of the time, so average joe can upload straight to flickr.