The treaty of Nystad from 1721 is obsolete and has been superseded by other treaties. Estonia[1], Latvia[2] and Lithuania[3] fought successful wars of independence against Russia in 1918-1919 and made peace treaties in which Russians recognized sovereignity and withdrew territorial claims. (These treaties were later violated when Russians entered a secret pact with Hitler and they jointly invaded everyone in Europe between Germany and Russia.)
Here's a helpful map visualizing how Russia and Germany divided Eastern Europe in the secret protocol[1] to the Hitler-Stalin pact: https://i.imgur.com/DvCrPWB.jpeg
As to the "Judenfrei" status, that's a great deal due to the executions and mass deportations[2] that Russians unleashed after invading in 1940. First they banned all Jewish organizations, even fraternities and tennis clubs. Then they started targeting the professional class (politicians, doctors, lawyers, etc) to wipe out people capable of running the country and challenge the Russian rule. Their crime was officially designated as "being socially undesirable". Jews were overrepresented among the victims by a factor of 10. By the time Germans arrived in 1941, only 900 Jews were left in Estonia, as depicted on your map. Some had been deported, others ran away wherever they could. The last 900 remained because they believed that Germans couldn't be worse than the Russian terror of 1940-1941.
When Russians invaded again in 1944 and began their 50-year occupation of the country (which included another wave of terror and mass deportations[3]), they replaced German antisemitic policies with their own and continued suppressing Jewish culture until the very end of the USSR. The Jewish school in Tallinn, for example, opened in 1924, was closed by Germans in 1941, and only in 1990, as the USSR entered the final death spiral, got its confiscated real estate back and resumed teaching. So if you intended to be clever and play the Jewish card, you chose a very wrong place to do it. Germans had the holocaust in store for them, and for Russians they were exploiters of the working class, destined for Siberian labor camps.
Soviet nomenclature did consist of Jews to significant extent. At times more, at times less, but it's disingenous for you to mention Jews being overrepresented among the victims without mentioning they were also overrepresented among Soviet officials, including high ranking ones.
Of course, it weren't these random religious small business owners but people significantly conditioned by the socialist regime, which they participated in creating.
https://en.wikipedia.org/wiki/The_Parrot_Speaking_Yiddish the movie highlights that fact: a Soviet military officer occupying Lithuania in 1939 turns out to be Jew, which does not preclude him from internment of the movie protagonist, also Jew and Polish army soldier at the time in the plot.
Indeed, one of the most notorious war criminals in "Judenfrei" Estonia was Idel Jakobson[1], a Latvian Jew, who in the 1930s tried to overthrow the democratic government, but got arrested and imprisoned. He was freed under 1938 general amnestia and left the country. Returned in 1940 with invading forces as a NKVD officer. In that role, he tortured and executed hundreds of notable public figures, including many Jewish businessmen. Excavations at mass execution sites have shown that his modus operandi was shooting his victims right in the face. The fact that Jakobson was still alive was discovered in 1996, but he died before the massive case against him could be brought to court.
[1] https://en.wikipedia.org/wiki/Treaty_of_Tartu_(Estonia%E2%80...
[2] https://en.wikipedia.org/wiki/Latvian%E2%80%93Soviet_Peace_T...
[3] https://en.wikipedia.org/wiki/Soviet%E2%80%93Lithuanian_Peac...