The outcome of the Native American removal was much worse than the Japanese internment camps. Would not compare that. I'm talking about the presidential act itself.
The presidential act itself was basically the same. "Force removal of an ethnic group from their homes and forced into a government controlled facility."
The reason the outcomes was different had no correlation with the president.
Deaths were lower because
1. A century of advancement in technology and medicine allows a safer way to kidnap and falsely imprison people. (Yes they were prisoners, people that tried to escape got killed)
2. Also people were a lot more humane in the 1900s than the 1800s so the people executing the order didn't have a high body count.
3. Much higher resistance from the native tribes than the Japanese Americans.