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Fixes and tweaks for `configure.ac` #3473

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Run time

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Job	Run time
Test Python 3.11 with MPI (true)	33m 21s
Test Python 3.9 with MPI (false)	22m 4s
Test Python 3.11 with MPI (false)	22m 46s
Test Python 3.9 with MPI (true)	33m 4s
	1h 51m 15s