The formula for absolute hydrostatic pressure on Earth is
$$ p = ρgh + p_{atm}, $$
where $ρ$ is the density of the liquid, $g$ is the gravitational acceleration, $h$ is the depth of the liquid, and $p_{atm}$ is the atmospheric pressure just above the surface of the liquid.
What I feel is that this formula and the concept that pressure of fluids (gasses and liquids) are isotropic are conflicting.
In the derivation of the formula, you say that, since the fluids are static, $ΣF=0$. Then you analyze the forces on column in the liquid and say that the atmospheric pressure contributes with the downwards pointing force $F_{atm}$, and the weight of the liquid column, pointing downwards, is $F_{g,column}$. To counter-act this force, the pressure of the liquid acts at the depth with an upwards-pointing force $F_{pressure}$. Then you express the resulting forces and get $$ ΣF=F_{pressure}-F_{g,column}-F_{atm}=0 $$ $$ \Leftrightarrow F_{pressure}=F_{g,column}+F_{atm} $$ $$ \Leftrightarrow \frac{F_{pressure}}{A}=\frac{F_{g,column}}{A}+\frac{F_{atm}}{A} $$ $$ \Leftrightarrow p=\frac{ρgV}{A}+p_{atm} $$ $$ \Leftrightarrow p=\frac{ρghA}{A}+p_{atm} $$ $$ \Leftrightarrow p=ρgh+p_{atm}. $$
The way I understand the isotropy of the atmospheric pressure is that the forces within the air at each given point points in all directions, so that each force vector is canceled out. This is why we don't get compressed by the kilometres of airs above us, which is pulled down by gravity, or pressure imbalances in the air; the resulting force at every point in the air is zero, because fluids distribute forces evenly throughout themselves.
But if that is the case, why does the atmospheric pressure affect the pressure in the liquid? In the derivation, the force of the atmospheric pressure points downwards AND its magnitude is EXACTLY equal to the atmospheric pressure just above the surface of the liquid (at sea level, it would be about $101325 Pa$). It feels like it should be irrelevant, since it is cancelled out by the isotropic nature of fluids. But it is an added constant in the formula, being derived from seeing it as an externally downwards pointing force.
How can these two facts coexist — the cancellation of the 'atmospheric force' via isotropy and its significance as an added constant in the formula for hydrostatic pressure, being equal to the atmospheric pressure?