I really can't say much to this except - this is what happens when a bunch of people get together to make spin-offs to a title they haven't worked on for years.
Chances are a lot of these inconsistencies are born from various parts of SE not properly communicating, writers and designers working partly off of memories and notes etc. not off of playing the original and sticking strictly to the plot of that.
I don't think it can be squared in terms of what you have - it can only be "head-cannoned", in in that regards I agree with the conclusions of your article.
Although, as you already know, personally I just pretend the compilation didn't happen, and then I don't have to square it to begin with =P
Also, excellent research, excellent article (although perhaps a bit dry =P, but that's to expect from the topic I guess)!