Like most questions on the Kuzari proof this question revolves around a different question. Can people rewrite history? The answer to that is "yes". The government, media and propagandists do it all the time. The Kuzari doesn't suggest otherwise.
What you can’t do is rewrite history when that revision (1)will force people to make both major personal and societal life changes while (2) you are insisting that that either you PERSONALLY saw those events take place or your ancestors personally saw those events and have ALREADY been keeping those personal and societal life changes even since the story place if the people you are speaking to never heard about your claims.
You can also probably convince people (with major difficulty of course) that a certain custom of unknown /unclear origin is kept for a made up reason but you would not be able to do so if the custom itself is inherently clear that it only exists to commemorate something. Which is the case by most of the mitzos that are zecher l’yitzas Mitzrayim.
Even propagandists and history rewriters have their limits of what they can sell. Such claims are going past the limits. E.g in today’s times both the stronger opponents and stronger supporters of Trump seem very eager to believe all sorts of baloney about him but you could never convince either group that his first inauguration never happened or that his second one did. Everyone being told that would know that if I did not see or hear about it already then it CAN not be true. That is what the Kuzari is saying.
Such an argument and those criteria do not apply to the Samaritan beliefs. There is nothing inherently preventing propagandists from retroactively claiming to have broke off from the main group during the times of Eli. There were no changes to Samaritan life being demanded by such a claim. What counterevidence would there have been at a much later time? At the much later date when this claim was being introduced anyone questioning “why didn’t I hear about it” would be given the same claim of superior knowledge that all propagandists and rewriters of history make.
As far as DNA is concerned it makes sense that there would be some shared DNA between Jews and Samaritans and that Samaritans would also have DNA like Jews do . At the time their status was unclear there were probably plenty of intermarriages. There also probably was a decent sized OTD crowd who became Samaritans. Additionally I have seen claims that the DNA evidence backs up the Jewish version of events .