[python/r] Move beyond the new-shape feature flag

[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:

These have been on by default for several weeks now. It's time to keep them.

Note there is another bit of logic (same files) around whether dense arrays can have current domain, which can't be removed until core 2.27 is released, and we move our core dependency to 2.27.

Notes for Reviewer:

This is less ambitious than #3259, which needs to wait until core 2.27.

[codecov]

Codecov Report

Attention: Patch coverage is 89.47368% with 2 lines in your changes missing coverage. Please review.

Project coverage is 85.48%. Comparing base (33b104c) to head (2c284cd).
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3301      +/-   ##
==========================================
+ Coverage   85.29%   85.48%   +0.18%     
==========================================
  Files          52       52              
  Lines        5517     5499      -18     
==========================================
- Hits         4706     4701       -5     
+ Misses        811      798      -13     

Flag	Coverage Δ
python	85.48% <89.47%> (+0.18%)	⬆️

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

Components	Coverage Δ
python_api	85.48% <89.47%> (+0.18%)	⬆️
libtiledbsoma	∅ <ø> (∅)