Set column order for GMT_IS_REFERENCE|GMT_VIA_VECTOR

[maxrjones]

Description of proposed changes

The column order was not set correctly for the GMT_IS_REFERENCE|GMT_VIA_VECTOR case. This is meant to fix that. GMT and PyGMT tests pass.

Fixes GenericMappingTools/pygmt#1440, relates to #5392

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[PaulWessel]

Thanks!