Hi Nobilangelo,
Currently, the model flip-axis and swap-axes options pertain to the importation of 3D models as a depthmap images and not the direct loading of images themselves. If you import an image or model that is noisy, or "spiky", you can smooth it out via the 'Project Setup' mode button (the mountain/sun photo icon at the top-left) and then by clicking "Input Size & Origin" on the left side of the window and then simply increment the "Smooth Radius" option that appears on the right side of the window and hit 'Apply'. This applies a gaussian blur to whatever input image you have: whether it be a loaded image file or an imported model.
The model import settings, insofar as the flip-axis and swap-axes options are concerned, the desired options must be set *before* you import the model, as they only apply to the model import process, not PixelCNC projects themselves, that's why those options are in the model import settings menu dialog and not the project setup panels. Once the model has been imported as a depthmap image you can set a smoothing radius and/or downscale factor per whatever smoothness you need to achieve to generate your toolpaths off of.
Within the next month or two I plan to expand PixelCNC's functionality so that users create a 'canvas' out of multiple images/models (if they wish to) which they can individually position, scale, rotate, flip, etc..