Issue and/or context: As tracked on issue #2407 / [sc-51048]. See also #3364.

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

Changes:

As found on #3244:

• The main context of [c++/python] Fixes for dense arrays and core 2.27/dev #3244 is:
  • For dense arrays only
  • If any dim's subarray range isn't specified, core uses the core domain
  • With new-shape feature-flag enabled, and with core 2.27 where dense arrays can have current domain (they couldn't in 2.26), we are indeed using data-sized core current domain and huge core domain
  • Put those together and we get these problems
  • Note there are a few other issues on this PR, and a few not yet included in this PR, other than that -- and those should be split out into separate PRs
• On this PR I've ben finding callsites, for write and for read, for Python and R, and touching up the ranges which end up being core subarrays on each dim slot
  • This is tedious and error-prone
• What we should do instead is:
  • In one place -- in libtiledbsoma, in ManagedQuery, before submit_query
  • If any dim's range has not been set up to this point, and if the array has a current domain, simply set the ranges on that dim to be the current domain's (lo, hi)
  • We know (for a fact) that core will go ahead and use the too-big domain anyway so this is safe

Notes for Reviewer: