I'd like to think that a vertical warp core is not a static component and a ship must be designed around it.
Many Star Fleet ships are primary hull saucers and separate nacelles, but not necessarily similar. I don't think the internal warp engine components must be identical from class to class.
The location of the reactor, the intermix shaft, the dilithium chamber, all that... I'd think it could be varied in accordance with each ship design. Just because a Constitution class featured a vertical intermix chamber, a Reliant-type probably would not, nor would a Grissom-type or a FJ Saladin or Hermes.
And then ENT showed a horizontal arrangement, so there you go. Other layouts of internal warp engine components should be possible with every class of ship.