So probably the key thing to keep in mind is that while anti-Jewish policies were a core component of the NDSAP platform, and started to be implemented quite soon after their rise to power, it was gradual. It wasn't as if all the Jews were rounded up and put in camps in 1933, let alone shipped off to the gas-chambers. There were many years of increasing restrictions and targeting. Many German Jews saw the writing on the wall very quickly, others took longer, but nevertheless realized that they had not future in Germany, and in both cases, the end result was that they left the country prior to the outbreak of World War II. It was often financially devastating for the Jews who left, as the Nazis did their best to prevent them from taking their wealth along with them, but it didn't stop several hundred thousand leaving the country by 1939. I've gone into some detail on this before, focusing on the Fromms, a wealthy Jewish family who owned a lucrative condom business in Germany at the time, so will quote an excerpt from an earlier answer I wrote:

As I noted, race was a key component of Hitler's ideas, and Nazi party philosophy in general, and anti-Jewish policies were implemented from the very start of Nazi rule in Germany as part of their push for "racial hygiene". Through the decade, Jews were kicked from the civil service, stripped of their citizenship, shunted from public life and employment, even stripped of their livelihoods, as Jewish owned businesses were forced to "Aryanize", that is, be sold to an Aryan owner at bottom-barrel price (with healthy profit for the state as well). Those who were able to emigrated, at great cost as they had to pay the "Reich Flight Tax". To look at one example detailed in the book "Fromms" by Gotz Aly, that one family alone show that in several stages of takeover of business and driving from Germny, the state profited a sum of 2,086,860.69 Reichsmark off of the Fromms family, although as some things aren't included in the official accounting, Aly estimates it might have gone over 3 million. This comes out, roughly, to 30 million Euros in spending power today (Aly's conversion, not my own) stolen by the state from just a single Jewish family and their business, and still, I believe, doesn't include the amount pilfered by the private individuals who "Aryanized" the company (which, for the prurient of you, made condoms).

On a larger scale, as mentioned in "Fromms", a single auction, held on on May 17, 1943, and selling off household goods taken from Jews who had been evicted from Berlin, netted 13 million Reichsmark (130 million Euros). In 1938 alone, the Reich Flight Tax brought in 340 million Reichsmark (assuming Aly is correct in conversion, that is 3.4 billion Euro or so), and the Flight Tax is only a small portion of the total income pilfered from the Jews. For comparison, when the Fromms left Germany, they paid 515,972.00 in Flight Tax, and that is only 1/4 of the total amount that they ended up turning over just to the state. So anyways, that was what was going on in the 1930s. Progressively harsher and harsher policies against the Jews, and many of them did flee, which really was fine with the Nazis as long as they had milked them for as much money as possible. But the same can't be said after 1939.

Even after the war began though, it still wasn't the immediate death warrant for the German Jews. The actual exterminations were not carried out in Germany itself, so once the decision was made to begin removing the German Jews from the country, the expulsion of the Jews from Germany towards the east was a slow one, and wasn't actually completed by the end of the war. Victor Klemperer, the famed diarist, was married to an Aryan woman, and although it meant that the quality of life for them was beyond abhorrent, he remained in Dresden until 1945, and although possibly would have been deported shortly, was able to get himself "lost" in the mass of refugees following the firebombing of the city that February (only the day prior he had been "enlisted" in delivering deportation notices to many of the remaining members of the city's Jewish community).

So anyways, the point of this is to say that the Jews of Germany had a very long time to get out of Germany. Some, unfortunately, didn't go far enough. Anne Frank's family is one example of German Jews who fled, only to find themselves in the path of the German war machine and again within the Nazi zone of control in 1940. But others did get far enough, and thus survived. Simply put, this wasn't an option for those in conquered territory. The Polish Jews, for instance, had no transitional period where they could have procured exit Visas and gotten away. Once they were under the German thumb, they were stuck, and had no significant way to escape the quickly worsening restrictions, and eventual implementation of the Final Solution. So basically, the chart you have is based off the German Jewish population in 1933, and includes all those ones who managed to get away. If the numbers were based off of 1939 statistics, it would be considerably higher, but still not at 100 percent, as noted.

And that's the sum of it. To give you a TLDR: German Jews had six years to realize how bad things were getting and go somewhere else. Jews in countries that got invaded didn't have that luxury.