It'd be incredibly tedious for most use cases of the tool if it resampled the output to match the input size.
The "shrinking" is affected by the "Pixelate" settings on the General tab, the other filtering is controlled by the rest of the controls and is applied alongside the pixelisation when exporting.
To get the swiping effect, just scale up the output from PixaTool using Nearest Neighbour, lay over the original image, and linear wipe between original and the PixaTool processed image, like this (PixaTool version a bit blurry because I f'd up the GIF conversion and was too lazy to re-encode for a simple example):