Update output shape and mean values from some x2sys_cross tests

[weiji14]

Description of proposed changes

Small changes to the number of output rows, and the mean value of the z_X and z_M/z_1/z_2 columns.

Also for test_x2sys_cross_input_dataframe_with_nan, a deep copy of the tracks: list[pd.DataFrame] object is now made before NaN values are set, to avoid some test flakiness.

Addresses #2961 (comment)

Reminders

• Run make format and make check to make sure the code follows the style guide.
• Add tests for new features or tests that would have caught the bug that you're fixing.
• Add new public functions/methods/classes to doc/api/index.rst.
• Write detailed docstrings for all functions/methods.
• If wrapping a new module, open a 'Wrap new GMT module' issue and submit reasonably-sized PRs.
• If adding new functionality, add an example to docstrings or tutorials.
• Use underscores (not hyphens) in names of Python files and directories.

Slash Commands

You can write slash commands (/command) in the first line of a comment to perform
specific operations. Supported slash command is:

• /format: automatically format and lint the code

[weiji14]

@seisman, this is similar to your commit f97d92e in #2936, but I used a deep copy (copy.deepcopy()) instead of a shallow copy (.copy()) because setting NaNs on the shallow copy newtracks still modified the original tracks object.

[weiji14]

Still a little unsure why GMT 6.5.0's x2sys_cross returns more rows than GMT 6.4.0. Might need to investigate.

[weiji14]

Haven't got time to check whether the change in output shape from x2sys_cross in GMT 6.5.0 mentioned at #2986 (comment) is ok or not, but gonna mark this ready for review so that we can merge this and get our test suite back to green.

[seisman]

Haven't got time to check whether the change in output shape from x2sys_cross in GMT 6.5.0 mentioned at #2986 (comment) is ok or not, but gonna mark this ready for review so that we can merge this and get our test suite back to green.

The x2sys_cross output change is caused by upstream PR GenericMappingTools/gmt#8188. So the new output is correct.