There seem to be two separate issues here: the legality of including the source code of a tool Sega/Atlus/TEA doesn't own the rights or license to, which is a technical/procedural concern; and the implications of the porting team using off-the-shelf third-party software to unpack and uprez game assets, which points to a quick and dirty port where quality doesn't seem to have been as high a priority as we'd like.
I feel like the legal issue is important to SEGA/Atlus/TEA and the creators of the third-party tool, but I don't know that it really affects anyone here. The latter concern, that this points to the porting process being done on the cheap with very little support from the original developers/publishers, concerns me more. Especially given that other Sega PC ports have been decent to great, it does raise questions about why Catherine is the way it is.