I can confirm this is currently the case by cross-referencing the coordinates in my raw 23andme data with dbSNP. (e.g. rs13096 is at coordinate 25359841, not 25206907)

Another question to clear up the confusion.. I am comparing the genotypes of rsIDs from the 23andme files versus the genotypes from snpedia.

23andme file for individual X:

on snpedia (for rs4988235):

on snpedia (for rs9939609):

after making some comparisons the results (i.e. the results i deduced):

if you noticed, in case of rs4988235 i flipped (i.e. converted) the genotype AA to TT because SNPedia shows that the orientation is minus, whereas i didn't flip the genotype for the rs9939609 because the orientation is plus.

So my question is, am I doing it the right way? I apologize if my question is naive, my background is in computer science not genomics.