I wasnt able to determine a way to change the default project directory at least in the locations I expected to be able to manually re-set this to a value other than the one originally selected. I will look into this further or possibly someone else on the forum can answer this question and hope to get back with you soon.
In regards to GUI color, this may be addressed in a future release of the product. I am still looking for an exact match on such behavior reported to Development. I was able to replicate unexpected behavior by simply changing the built in Gnome theme from the default (Clearlooks I think) to the High Contrast Inverse theme. As far as I am aware there is not an easy way of changing how Amplifier responds. However, in the config/display directory is a config file where RGB colors for various aspect can be changed. However, not all aspects may be customized and this is not really a supported method of customization. This is probably another good enhancement request to be able to customize this via the GUI or pick up the theme better and play nice.
The data limit is by default set to 100MB. You can change this either in the GUI via Project Properties or at the command line using the -data-limit option.