Based on manufacturer claims of what their commercial products accomplish (and noting that we lack any independent testing of any of these products or the associated claims), the net effect of perfect implementation of Balling and perfect implementation of a two part is essentially the same. It was pointed out to me by Tropic Marin that Balling can have a somewhat smaller effect on salinity over time and that could be true (both raise salinity).
Otherwise, there's no theoretical difference. Balling puts the sodium chloride free salt in a third part, and a two part such as B-ionic distributes the ingredients of the sodium chloride free salt mix among the two parts.
How well any company meets the perfect claims remains unknown to me, but personally I doubt that any reefer will see a substantial difference between high quality commercial two parts and Balling except in that some will impact pH in different ways and, as noted, may have less different impacts on salinity over time. Potency will certainly vary between brands too.
Also, neither of these two methods should be assumed to preclude the need or potential benefit, anyway, of trace element additives.