To put it simply, the Honda (insert: "Kawasaki") engineers calculated everything dozens of different ways, to come up with the best set of compromises, for the best economic performance, overall.
That seems to preclude any modifications whatsoever -- they "engineered" the whole bike. "Value engineering", as you say? And some folks might not agree on "best". For starters.
Suspension allows manufacturers to play games, to save money. The fuel system, is another matter, altogether! They can't take shortcuts, with that.
Well, they can. And they do.
But I hear you, that you're limiting this to the "fuel system", including the whole induction and exhaust systems. And I generally agree with that: it's kinda silly to think we can "dial in" more performance
at all, much less to do that without upsetting some other performance compromise -- as if we're the only ones to notice the adjusters.
Folks wrongly think that pods flow more air than an engineered airbox, even if more air is necessarily good (I'm thinking of uniform air flow). I used to think that too; and I've wasted money on pod filters.
I "generally agree", but this isn't always true. One compromise I encountered (different bike) was an undersized air box. Like others before me, we found a noticeable performance increase (particularly throttle snap) by drilling lots of holes in the airbox. (Also had to fuss with jetting, which became very complicated because it was a single-cylinder bike but had two carbs, of totally different designs. A major nightmare. But it really is better after all. And I had to fuss with the jetting anyway, mostly because it came heinously lean.) And many have improved performance by adjusting carb settings, even if these adjustments were plugged at the factory. Especially those of us living at high elevations, where lots of compromises get compromised.
But for the simple modification I had in mind, I didn't expect any performance effect at all. It was an aesthetic issue: I disagree with the apparent original compromise. I want a
little more exhaust note. And I don't want an XII just like everyone else's.
I edited my original post after looking closer and finding that this exhaust system is more complicated than I expected. As you suggest, I'm not going to screw with it any more. But it could've gone the other way: the complicated plumbing might not have involved the tips (as I expected), and switching the tips out could have been simple and fun. I wish I'd looked closer before making that cut, but it's easy to put back. No harm, no foul.
(Still want a bit more exhaust note, if not a more induction "noise". And still won't hesitate to make the bike mine.)