Then there are the Torchwood and NuWho complications of the Tardii being spaceborne coral creatures carved for use. With them flipping back and forwards between it being a sentient "she" to a highly tempermental sentient AI "it".
From the Eye of Harmony being on Gallifrey and the corresponding room on the TARDIS being an energy receptor, to it being a literal Eye on the ship, that between the Tenth Doctor (TARDIS running out of power, Eye useless) to having a newly implaced 'permanently dying' (WTH even?) star somehow installed by the Doctor alone.
Which either needs a new second, larger "bigger on the inside" pocket dimension nearly 1 AU in size, or some funky spatial compression to make everything smaller, requiring a new massive room to accomodate it. (Shown in JttCotT console to be much larger than even the engine room).
So it's either a living entity of finite size with cybernetic implants early in it's life, the Replicator Tree from 'Journey' allowing it to use the Eye's energy to materialise new rooms in hours. Coupled with near infinite ability to create new pocket dimensions.
Or a machine through and through using it to build more of itself, including the ability to accomodate an entire star and it's habitable (ish) zone inside as needed.
Better to just say "magic" and leave it.
Well, I tend to take the tact that the ship itself is a construct of living metal. It's interior dimension is a single pocket universe within itself. Being made of living metal means it can also act as a transmitter for vibrational waves, needing no central area for additional room generation, since it can broadcast that signal throughout it's entire structure, not to mention communication signals, and openings to the main entrance section outer plasmic shell (via River song's fall in the pool) to any other area desired. the eye of harmony I am okay with that being a source of unlimited energy, but that infinite energy being needed to support the Dimension, and not directly related to fueling the engines themselves. I mean if you are going to create an artificial pocket universe with near infinite energy, then that will pretty much take up most of that considering the infinite nature of the dimensional pocket, and the fact that you have to allocate time from the beginning of that dimension to it's end of existence, which means an additional source is needed to fuel those engines.
infinite not meaning infinitely allocated to all aspects of the ship. I think that the coral is a mask, or chameleon form of the living metal, or maybe a base material, which resides within each architectural configuration holding orbs. Coral was and still is of actual canon just part of the architectural configuration for the console room desk top, and since that part of the show where the meta crisis doctor receiving coral to build his own, was never really aired, I tend to see that as just "magic Coral" which isn't truly real, IMHO. I have spent the last 10 years or so studying physics, and reading anything I can on electromagnetism, and gravity, and particle physics, not to mention researching Doctor who classic, and the theories of others online..etc..etc.
My point is that I am applying real world physics to this endeavor, and though I am happy to hear that same old and rather over used phrase once more "magic Box" as a scifi fan, and not a fantasy fan, I prefer the practical approach to Doctor Who, rather then the oblivious. I want to believe what I see, and can not bring myself to just count it as simply a good story.