Sure it is. You must first pick the target(s) of such spells, and if the number of targets is an effect that can be modified (which must occur before any attack rolls can take place), then any subsequent rolls to see exactly what happens to said target(s) must therefore be effects of that choice. The feats even call out saving throws and opposed rolls as not being allowed to be modified, with no indication that they are not effects, and instead merely exemptions to the benefits of the feats. Take Ray of Enfeeblement, for instance. The attack roll is stated right in the "effects" portion of the spell. It is the first numeric, variable effect of the spell. The penalty to any hit target's strength is the second. Yes, one effect is reliant on the other to first succeed, but that does not change the fact that the first is still an effect of the spell.
Your argument is correct with regards to things like spell failure and concentration checks, because they are not governed by the spell itself, but rather the act of casting a spell, regardless of what its effects might be, including choosing targets or the location of the area or such.
