Many molecular biology recipes use MgSO4 (and not MgCl2). Is there indeed a preference? If so, why?
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My guess is its the solubility properties of the anions.
Chloride ions can precipitate with some metals that might appear in a complicated buffer or medium. And yes they could even compete with enzyme binding. Sulfate will remain in solution with just about anything.
There are exceptions, but if you're making a buffer you're probably going to do better if you use the general solubility rules.