get_xspectra_structures: Refactor and Improve Code

Refactors major components of `get_xspectra_structures` as part of
ongoing improvement work. These changes are the first of two
improvements intended to enable users to set symmetry data manually
instead of relying on automatic symmetry analysis - ultimately enabling
the same feature for the `XspectraCrystalWorkChain` and any others which
use the same structure preparation tools.

Changes:
* Moves supercell creation, processes for molecules, and generation of
  `equivalent_sites_data` to separate functions.
* Adds functionality for users to manually provide symmetry data, thus
  enabling the `CalcFunction` to be used as a means to generate structures
 with user control over which exact sites to mark.
* Fixes a bug discovered in the case where non-hubbard structures with
  custom Kind names lost their Kind names when converting the ASE
supercell to `StructureData` type.
* Fixes a small oversight in the tests where `spglib_settings` was
  mistakenly named `spglib_options`.