"We say, Electric Flux, ππΈ=πΈπcos(π) where π is the angle between E and S. However, there is another definition for the same..."
No. There is not another definition.
The electric flux, $d\Phi$, through a surface element, $d\mathbf S$, is defined by
$$d\Phi=\mathbf E.d\mathbf S$$
Gauss's law states that the net flux emerging through a closed surface S is related to the algebraic sum, $Q$, of the charge enclosed by S, according to
$$\int_S d\Phi = \frac 1 {\epsilon_0} Q$$
This is not a definition but a law. If the charges are stationary, it may be deduced from Coulomb's law, but it also applies if the charges are moving, so it is a law in its own right.
It is, indeed, remarkable that if we compute the integral over different surfaces enclosing $Q$, we get the same resultant flux for each surface. You should try starting with a very simple case: spherical Gaussian surfaces of different radii with a single stationary charge at the centre.
"Effectively one can say that electric flux depends on the electric field, Surface Area (i.e. geometry) and charge enclosed (by gaussian surface)."
Perhaps one could say this, but it would be clearer to say that if we know the electric field strength at all points on a closed surface, S, we can calculate the resultant flux through S by applying the definition of $d\Phi$ and integrating over S, OR if we know the charges inside S, we can calculate the resultant flux through S using Gauss's law. 'OR' is more appropriate than 'AND'.
Your statement is rather like saying that the total number of limbs possessed by a group of able-bodied people depends on the number of arms + the number of legs AND on the number of people.
[The definition of a limb is an arm or a leg. Wood's law of limbs is that an able-bodied person has 4 limbs. We can calculate the total number of limbs either from the definition (by direct counting of arms and legs) or the law (simply by counting people and multiplying by 4).]