(1) Yes, there are functional differences between the varying types of regional hypertrophy, both when considering increases in fiber length vs. diameter, and also when considering growth in different functional compartments.
The difference in functional effects of fiber length vs. diameter is perhaps best appreciated by comparing the effects of full and partial range of motion strength training.
Regional growth in compartments relates directly to the function that each compartment has evolved to perform. For example, hypertrophy of the medial region of the vastus lateralis is related to increased squat 1RM, but hypertrophy of the central region is not.
https://www.ncbi.nlm.nih.gov/pubmed/24616036
(2) Yes, hypetrophy research is limited when measuring muscle cross-sectional area. Measurements of muscle volume are a much better approach, since they take account of the differences in responses between fiber length and volume between exercises, loading types, and individuals.
