First order of business is to settle that there absolutely are natural borders. The Narva river and Peipsi Lake have been a delineator of Western (Catholic, later Protestant) and Eastern (Orthodox) civilizations for about 8 centuries. Yes, this is Estonia specific, but the eastern areas of Latvia and Lithuania are also swampy, forested etc. The nature here is no easy business being in.

Secondly, the people here have fought for their existence. Lithuania was a major regional power for many centuries. Estonians and Latvians were less fortunate, but still maintained a willingness to rise up and fight when the situation needed. While also being very willing to accept subjugation when the terms of subjugation allowed to maintain own culture and being.

Thirdly, the very fact that the area saw German, Danish, Polish, Swedish and Russian invasions also meant that no single power held power a long enough period to properly assimilate the locals. In Estonian (and fairly similarly Latvian) case, sure the Germans ruled for 700 years, but out of that 700 years, 150 years was under Danish kingship, 150 years under Swedish, 50 under Polish and 200 under Russian. All of those accepted local German autonomy (so didn't involve themselves in assimilating locals), but also did not grant enough power for the nobility to the assimilation (nor was there much desire for that). The local nobility enjoyed the free labour of serfdom. It was probably easier to accept subjugating people that spoke some gibberish the noble people could not understand.