Take it easier :)
Pressure at some level is weight of surrounding medium on top of it (density x volume), divided by surface area - surface cancels out, leaving us with some unknown height H.
Pressure at some lower level (down by h) is almost the same, but instead H we can use H + h.
Pressure difference is related to H + h - H = h (times the density times the volume divided by surface area - which are constants for given situation) (multiplied to different parameters, which are constants for given situation).
In general, physics theories and formulas are just models of real world. We can have different models for same phenomenon, we only need to know, on which conditions we can use simpler models and when we cannot - this is a bit intuitive; otherwise you have to prove classical formulas using QFT (which is yet another model - most certainly not the final one) and you will sink into complex math and likely can't grasp general and simple principles from there. Or if you can, then you are very lucky one and can apply to some leading position in Princeton or so :)
Like your friend said - "Different layers of explanation are appropriate for different purposes" - he was exactly right :)
In context of buoyancy you can treat surrounding medium as ideal fluid, you don't need neither molecular theory nor QFT.