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On an empty stomach, insulin levels should be lower. According to the following study, cells absorb more magnesium when there's insulin. https://www.ncbi.nlm.nih.gov/pubmed/8861135

Also, most of our magnesium is stored in our cells that RBC magnesium levels are more reliable than serum levels in terms of magnesium status.

Does that mean it's better to take magnesium with carbohydrates (unrefined of course) which increases insulin than on an empty stomach?

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The article you've linked mentions impaired magnesium uptake in diabetes mellitus type 2, not in healthy individuals.

In cases when meals significantly affect bioavailability of a supplement, there will be likely an instruction on the information leaflet about the optimal time to take it.

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