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.