I agree that reading is a complex process, and it is very unlikely that one learning activity will be sufficient for a student to learn the entire process. However, it is quite possible for a learning activity, if well designed, to teach a specific component of the reading process. Thus a student's reading is improved.
I also agree that an important component of instructional design is a thorough analysis of the target audience. This analysis may be quite different for commercial developers and instructional designers. Commercial developers typically make design decisions based on the "market." They are very interested in "what sells their software to the most people." Instructional designers usually, hopefully always, consider the instructional needs of their target audience and primarily make decisions based on the "student." They are very interested in "what methodology provides the most effective and efficient instruction."
In both cases, decisions must be made to include or exclude specific types of students. To make these decisions, specific learner and/or market characteristics must be considered. It is true that there exist a vast range of individual differences, but it is possible to select the characteristics that are most relevant.
Of course it would be wonderful to create instructional software that is effective for every student, but this is impossible. Therefore different instructional methodology is used, and different instructional materials are developed. In this way, specific instructional methods may be used with the dyslexic and still different methods for the hearing impaired.
The opportunity for people to create instructional materials for different target audiences is great. It would be nice if one day there were instructional materials that meet everyone's needs.