Yeah, a stadivarius ? yes, a cue and a violin, almost the same thing. What diff does it matter what shaft he puts on it ? If he likes one better, why would he not use it. Like you said, it matters not what butt it is, so put the best shaft on the prettiest butt and that's your cue.
Plus, when he goes to sell in 5 or 10 years, the original shafts will be MINT, unchalked condition, and thus cue will be worth more. Kind of a win/win. '
Heck, many custom cuemakers will fit an LD shaft to the cue if you prefer it that way. Why do they care if you like an LD shaft or not, as long as the check clears.