yes, a 5-piece laminated neck with certain grain alignment will be stiffer than a comparable single piece and this may change the tone slightly. but it really is just generalisations so we cant be as specific as you want without knowing the individual piece of wood
i think (and it is just opinion based on the wood i have worked with) the bubinga/ebony neck will give you a fast, strong attack.
i wouldnt rule out a maple cap if its what you want, but personally i would keep it as a thin one so its tonal impact is reduced.
I find bubinga quite forgiving really and i think you are over thinking things, sure it can be bright... but its not harsh
Here is a FF baritone i made totally out of bubinga, maple, wenge & ebony, all hard, heavy, 'bright' woods. the thing i think it has is clarity and a strong tone across the frequencies