The standard reaction enthalpy you have describe is only for a pure substance if you are talking about a standard enthalpy of formation. Otherwise the equation wouldn't be valid for reactions that have more than one product, right? In the specific case of a standard enthalpy of formation, you are talking about the enthalpy change associated with the creation of one mole of a pure substance from its component elements in their standard states. This gets at your second question ... the zero on the enthalpy scale is established by convention (and this is the reason why the definition of standard enthalpy of formation works) ... the standard enthalpy of formation of an element in its standard state is DEFINED to be zero.
Now, you can estimate the standard reaction enthalpy for any chemical reaction by subtracting the summed standard enthalpies of formation of the reactants from the summed standard enthalpies of formation of the products, taking into account the appropriate stoichiometric coefficients from the balanced chemical equation. That process is similar to what you have written, but not precisely the same, since you omitted the stoichiometry information (and the chemical equation, for that matter). The standard enthalpy estimate obtained will pertain to reactions carried out at the given conditions .. standard enthalpies are defined for 1 atm pressure but variable temperature, so you may need to correct tabulated standard enthalpies of formation to match the given reaction conditions.
One last point is that enthalpy is absolutely defined as a thermodynamic quantity .. it is the internal energy plus the product of pressure and volume, $H=U + pV$. The issue is that the internal energy of a substance is hard to define absolutely .. are you going to include the binding energies of the core electrons to their atoms? How about the strong forces holding the nuclei together? Thus for chemical processes it almost always makes sense to deal with just changes in enthalpy, since most of the really low level stuff I mentioned doesn't change between reactants and products. I think that may have been part of what you were getting at with your second question.