Personally, I think that more advanced technology for the Houses is an excellent thing for a mod to do. It does not seem logical, for example, that Liberty, being so close to all the Independent Worlds, and Rheinland, the most powerful House in vanilla FL, would be content to have crappy little waterguns and tin cans for their "navy." If you stock a vanilla Defender with the max guns Liberty offers and put it up against a Valkyrie, decked with Rheinland's best guns, (neither of which can actually mount the best in the House, which doesn't make any sense to begin with), the Valkyrie is going to vape the Defender (rip right into that piss-poor 1600 hull [10] ).
So, I do not think that balancing all the stock House fighters is a bad idea. Making more advanced versions to make "House fights" (or just traveling to Border Worlds/Hispania) more feasible and fair is also a good idea.
Microsoft and DA did a fantastic job on Freelancer as a whole, but they sure left the Houses wanting for some major balancing ... So they left the fun of modding and doing things such as that to us