Ok solved it - referencing for anyone else in future affected. Credit to steam forum tough for solution, happened to find the post solving it.
6.3x should be the correct math if you have Deacon cloak and dagger perk, maxed out mister sandman, and maxed out ninja for total of 6.3x sneak attack multiplier.
But game is bugged, or at least in some people's cases get bugged and does not multiple the different pieces together correctly. Math is math - 4x3 should be same as 3x4, but in FO4, the order in which you took the perks matter for this bug.
To get 6.3x instead of the bugged 5.9x, need to take the perks in order so that Ninja comes after sandman. Steam forum post said had to also have Deacon perk first but personally I didn't find that to be the case. Using console commands, removed all MS and all Ninja. Then re-added MS, then re-added Ninja. I believe it is only the last rank the matters because in first PT where I had this work ok, believe I took couple points in each, but took final 3rd rank of Ninja last.
So if you have 5.9x with all perks instead of the correct additive math of 6.3x, can live with it or use console (if available), to remove MS and Ninja perks, then re-add so that Ninja 3rd rank is last.