[python] Re-run, and update, example notebooks with new shape feature

[johnkerl]

Issue and/or context: As tracked on issue #2407 / [sc-51048].

Note that the intended Python and R API changes are all agreed on and finalized as described in #2407.

Changes:

Re-execute our notebooks with the new-shape feature. Change the wording in many places to remove needless complexities from the pre-shape era.

This PR affects existing notebooks. There is a separate PR with a new notebook dedicated to the new shape feature: #3294.

Notes for Reviewer:

This PR was run on a system with core dev (2.27-to-be) installed on it.

Handy review link with rendered notebooks:
https://github.com/single-cell-data/TileDB-SOMA/tree/kerl/notebook-new-shape-refresh/apis/python/notebooks

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.40%. Comparing base (0dea435) to head (23953ae).
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3290      +/-   ##
==========================================
+ Coverage   85.29%   85.40%   +0.10%     
==========================================
  Files          52       52              
  Lines        5517     5517              
==========================================
+ Hits         4706     4712       +6     
+ Misses        811      805       -6     

Flag	Coverage Δ
python	85.40% <ø> (+0.10%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
python_api	85.40% <ø> (+0.10%)	⬆️
libtiledbsoma	∅ <ø> (∅)

[johnkerl]

Converting to draft while I rework the data storage on a separate PR

[johnkerl]

@aaronwolen re-requesting review as this is now rebased on top of #3295 (which has been merged).