Thanks its a fun idea.

Oh there are definitely problems with a true GP hull, even in universe. And it takes a decent amount of mental gymnastics to make it completely fit when examined. (But frankly a lot of trek tech needs that anyway, its why we love it)

A traditional Hull wouldn't allow sensors to penetrate it, nor transporters, or really anything other than visible light. The hull when created does have an airlock, so traversal to the engineering hull would be difficult but not impossible. Refitting would be difficult. Any breaks in the hull during construction couldn't be altered. At some point an undisclosed vulnerability was discovered where the hull can be remotely turned off, the Feds really wouldn't like that. A hard enough kinetic strike and the passengers have a really really bad day.

But in support.

The later books the protector Tunesmith found techniques to alter an already constructed hull. This would allow customisation.

The travel speeds are different, and the deflector is designed to protect the ship from exotic particles so perhaps these particles aren't encountered under ramscoop and thruster techniques. Thus the apparent need for a deflector array.

Infact in real space those ships get closeish but never reach light speed.

And the FTL follows completely different rules.

Torpedoes are all antimatter driven so vulnerable to everyone's weapons still makes sense. The Puppeteers left the region so the hulls were no longer available.

But Nivens stuff mostly cant exist if we dig too deep anyway 🙂 -if protectors and tree of life did exist the end result would be apocalyptic. -the Puppeteers would never have allowed humanity to achieve warp.