Views-overriden taxonomy/term page returns not found
I was able to solve this only by duplicating the "taxonomy" view. This view's argument configuration makes it a viable solution. 

After configuring/enabling this view, you can set the taxonomy url aliases to work in the same way.

A working example: http://www.indice.gr/portfolio/all shows "all" projects, wheras http://www.indice.gr/portfolio/mobile-application shows projects under the mobile-application term. Yay!