TST: adapt a coordinates test to numpy 2

[neutrinoceros]

Description

This pull request is to address part of #16423 (specifically coordinates).

The first commit is shared with #16426 so there should be no conflicts between these two.

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[github-actions]

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[neutrinoceros]

The io.misc label should be removed.

[pllim]

Looks uncontroversial enough now. Thanks!