EDIT
I found that a similar question was asked by user Muno in this question in a follow up comment which is as follows (in short this is what I'm asking for)
to make my question more succinct: if buoyant force depends on a difference in pressure, and pressure at a particular depth depends upon the weight above it, why isn't a submerged object's weight factored into pressure?
I have heard of the reason that water applies buoyant force due to a gradient of pressure. But why does it arise?
Consider the following (the cause of my problem)
When analyzing the situation it's said that the object feels a force which is equal to the weight of water that it displaces. But I'm a bit (or say too much) confused on this too. It's as follows :
The water above the object (say at a depth $h_a$) is applying a force equal to its weight which is $\pi r^2 h \rho _{water}$. Now consider the lower portion, the object and the water column above are applying a force equal to
$$\pi r^2 h \rho _\text{water} g+W_\text{object}$$
but the water column below is applying a force equals to
$$-(\pi r^2 h \rho _\text{water} g +W_\text{object})$$ (via Newton's third law)
therefore the net force on the object is $-W_\text{object}$. So why is this not the case?