feat(io): optional z-coordinate passthrough (include_z, default False)

[EliHei2]

Add an include_z preprocessor parameter (threaded through get_preprocessor); when enabled the transcript z coordinate is carried into the standardized output. Defaults to False so base behaviour is unchanged. Independent of the QV change.

[Tobiaspk]

It looks like rename_map is defined in the Xenium preprocessor but used in CosMX. Probably should be switched. Just two questions:

• Should this be automatically inferred, or be a user input in the future?
• z is not yet used downstream. How should it affect the model? [main] Feature: SpatialData I/O support #37 suggests to use it during setup_transcripts_graph and setup_predictions_graph. Will defer to you @EliHei2 and @andrewmoorman

[Tobiaspk]

A couple more considerations: how does including z impact accuracy vs. memory and time cost? My concern is that kNN etc. might explode, we should avoid that.