For your first question, They can vary dramatically.
I did not originally post as a formal answer because my statement below is hard to cite a source and would therefore be somewhat subjective, although I am pretty confident in the assertion. It is based on my own experience in both GWAS and EWAS literature reading. My research concerns methods for analysis of such data.
To answer your second question, the main focus has shifted from genetic variation (still done though) to expression variation and epigenetic variation. The expression research focuses exactly on the type of issue you are discussing with alternative splicing, and this is largely possible because of the decrease of the cost of RNAseq. We aren't as fixated on sequence anymore; the advent of GWAS, once thought to be a panacea for the explanation of disease susceptibility has only ended up explaining a fraction of genetic heritability estimates. Not to say it isn't focused on, just in the context of other types of variation and environmental exposures.