First thoughts.
You have posted in the right place, and seem to have included all the important information.
Some questions that might help sort out the problem, and I don't know the answers.
1. Can you find Jacob Whitaker's daughter Julia Ann and eliminate her from being a daughter in law? Did people on the Freedmen's Bureau records name daughters-in-law as children? I would guess not, but I don't know.
2. Are there any other records regarding Ruben Whitaker's death that might name his siblings? I'm thinking of one of those hand-out life stories from African-American funeral homes that were used because the papers wouldn't print an obit. Or can you learn his siblings somehow else? Did Ruben move to Alabama? to the same place as your Levi?
3. Regarding the Juli Anna who received the pension: for what war? Your Levi was too young for the American Civil War and probably too old, and settled down, for the Spanish-American war. Were there even pensions for the Sp-Amer War?
Can you tell if Juli Anna is white or black? All a part of a general strategy to eliminate this Levi. Find out as much about him as you can, and you may be able to eliminate him.
4. Were there naming patterns in Black southern families? In other words, did your Levi Whitaker name any children Jacob and Melvina?
5. You seem to have really "done your homework", so you might already have these resources:
This lady seems to know what she is talking about, I just haven't needed the information yet:
https://www.reclaimingkin.com/strategy-pension-records/also
https://www.reclaimingkin.com/southern-plantations/She would probably be willing to answer your questions as well, but I don't know for sure.
background info on "Records" she mentions:
https://www.worldcat.org/title/records-of-ante-bellum-southern-plantations-from-the-revolution-through-the-civil-war/oclc/12894903I have a few of the indexes, but not the one for Georgia. Googling "lexisnexis antebellum south plantation series" turned up a lot of them, but I didn't find Alabama.
Tony Burroughs book, Black Roots, helped me get as far as I did with one of my friend's Black families. He might have a newer book out by now.