Since I was not able to get an online copy of that Midrash cited, I could only go on what part of the explanation was:
"This parallels a shift in the Septuagint’s translation of Hebrew “pelistim”. Before Judges, it uses the neutral transliteration “phulistiim”, but beginning with Judges it switches to the pejorative “allophuloi”.
The problem here is that the Septuagint uses the legitimate name of “pelistim” or “phulistiim” during the period where they did not exist on the Levantine coast… and starts to use another terminology in Judges which is when the Philistines were actually present to exert their influence.
The rabbinical sources don’t appear to have any extra-Biblical historical reasons to consider the Philistines of Genesis to be a reference to a completely different people.
The rabbinical reasoning for the Philistines being a separate group is not archaeological. They are arguing why the Israelites don’t have to honor a treaty made with the so-called “older” group.
And the synonyms being used instead of Philistines (in the LXX and elsewhere) are terms for the RECENT Philistines… not the bunch that Abraham knew. Which is the exact opposite of the situation. If there were real Philistines (aka, the Pelest) it was after Exodus, not back in Abraham’s day.
In Abraham’s day, the Egyptian army and diplomatic corp were all over Canaan… including the Philistine coast (Canaanites lived on that part of the Coast at that time).
And yet we see no evidence of Egyptian troops, tax collectors and plantation managers anywhere in the Old Testament … until a Pharaoh mysteriously arrives and disappears long enough to capture Gezer and give it to Solomon’s wife.
In reality, Egypt would have been doing things like that from the time of the Hyksos expulsion until the settlement of the Pelest (sometime around 1150 BCE to 1130 BCE).
After 1130 BCE, the Egyptians were penned up on the other side of the Sinai by the Philistines.