Do rules from one of the Sudoku grids have affects to digits in in one of the other four grids? For example, If the centre grid of the first samurai sudoku is non consecutive, does that also hold for digits in an overlapping 3x3 box with neighbours that are only in one of the other four grids?
No. The rules of the Sudoku must be satisfied within the 9x9 Sudoku.
If you separate out the Samurai into the five individual 9x9 grids, they must satisfy the variant rules within the individual grid.