The electric field in the following case, at the sphere, is due to
$q_1+q_2$ or $q_1+q_2+q_3$.
It is due to all three charges.
The electric field at a point on the sphere, or for that matter at any any location in the diagram, equals the vector sum of the electric field contributions of all three point charges. See FIG 1 below showing the electric field lines of all three charges (assumed positive) at point A of the sphere, which vectorially sum up to equal the field at that point.
So if we calculate the electric field by dividing flux with the area
of Gaussian surface, the electric field is due to all charges or just
$q_1$ and $q_2$.
Only if you have symmetry, such as if the enclosed charge was a point charge at the center of the sphere, and there were no field contributions from external charges, can you divide the net flux by the total area to get the magnitude of the electric field, because the field would be the same at each point on the surface. The net flux is, however, only due to the charge enclosed. $q3$ contributes no net flux because the total flux of the field lines into the space enclosed by the surface equals the total flux of the lines out of the space for a net flux of zero. See FIG 2.
Hope this helps.