Are they different flavors? I get fantastic throat hit out of my DIY menthol but...well, it's menthol. It would have great throat hit at 0 mg.
If the same flavor, there's probably a little variance in their mixing methods, or they've been steeped for different periods of time. Liquids tend to lose any harsh notes they have from steeping, so fresh e-liquids will always have just a touch more throat hit.