Interesting take. The genetics in my view could hardly be a proof of ethnicity though as I feel we are very mixed on the Balkans. However I don't think the Pomak-BG difference could be big (if any). I suppose its like how a regional group (for example Moesians) compares to the Bulgarians as a whole. There would be differences of course. Maybe more so with the Pomaks, which till recently, were more close off and the intermarriages with other Bulgarians were more rare, due to religion, no doubt.
As for if Pomaks are absorbed in the Bulgarian society: I would say yes (younger ones at least), but there are some of course who prefer to stick to their society and to not intermarry with other Bulgarians. I had an acquaintance - Bulgarian pomak, who was religious (very observing muslim) who did see himself as somewhat different to the main body of Bulgarians (at least I got that impression), but said his sister was not religious, married to Bulgarian and he said she felt like Bulgarian nationally. So I guess it depends on the person really.
There have been clashes somewhat between Pomaks and orthodox Bulgarians historically, but I d say that doesn't prove we have different origin. Just look at the Macedono-Bulgarian relations in the last 50 years...
Its strange how on the Balkans the religion is stronger factor than say language/culture/ethnicity. Just look how the Bulgarians in Northern Greece were Hellenized or how Greeks in Southern Black Sea coast were Bulgarized. Its astonishing that those different ethnicities became part of the main ethnicity, into which country they decided to stay. I d say its due to the same religion. The Pomaks still are in a sense closed off to other Bulgarians (or it is probably both ways), cause of the religion. The only Balkan group who managed to integrate its people from all faiths, strangely enough, is the Albanians.
As for the language: maybe because of this closeness, the Pomaks in a way have managed to retain their dialect (not that different to official Bulgarian though). The main difference is that they have retained more Turkish words, which were until recently shared with other Bulgarians, but in the 20th century those words were replaced in the official Bulgarian with Russian or western ones. I know those old Turkish words (that disappeared in official Bulgarian), but they sound simply archaic.
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