To answer the original question, flattening without something like a drum sander, planer, or even a belt sander is pretty difficult. Your pieces have to be dead flat and aligned as well as can be, otherwise you'll be sanding for hours. Beyond that, it won't be perfectly flat, and enough so that you might get gaps in gluing. Even something like a router sled would work for flattening.
If you have that much of a problem with snipe, you should probably work on a different setup and/or improve your technique. Lifting the back of the board as you feed (and the front as it comes out) helps reduce snipe. Also, as mentioned before, what I usually do, whether I'm making long grain or end grain boards, I add extra length. On long grain (the final step of a long grain board, or the middle step of an end grain board) I add two longer strips. For example, if it's supposed to be a 20" cutting board, two of the strips (towards the outside, if not the outermost edge) will be 24" or so to prevent snipe. Similarly, on an end grain board, it's pretty difficult to avoid all tearout while flattening so I generally plan on a bit more length than I actually want.
I have never tried to surface end grain with knives, only helical, so I can't speak to that. Even so, helical heads require very light passes.
If you have that much of a problem with snipe, you should probably work on a different setup and/or improve your technique. Lifting the back of the board as you feed (and the front as it comes out) helps reduce snipe. Also, as mentioned before, what I usually do, whether I'm making long grain or end grain boards, I add extra length. On long grain (the final step of a long grain board, or the middle step of an end grain board) I add two longer strips. For example, if it's supposed to be a 20" cutting board, two of the strips (towards the outside, if not the outermost edge) will be 24" or so to prevent snipe. Similarly, on an end grain board, it's pretty difficult to avoid all tearout while flattening so I generally plan on a bit more length than I actually want.
I have never tried to surface end grain with knives, only helical, so I can't speak to that. Even so, helical heads require very light passes.