Ah, check, I get what you're saying. But for non-index pages, the search box (basically the only function button that can be on the right, I believe) will never be shown anyway, so for the non-index pages, the menu is now always going to be centered, whereas for regular index-pages, it depends on whether the user has checked the "Use search" setting or not.
I think that the best solution would be to add a specific setting, "Navigation menu alignment" or something like that, where the user could choose between "left" and "centered" (maybe even "right"), and then both index-pages and non-index-pages would use that setting for a consistent look & feel.
For me personally, right now I simply added the custom CSS, and since I also wanted the search box to appear on non-index pages, I edited top-bar.inc and changed
hasTopBarRight = (_useSearch && !moveSearchToHero) && pageType !== 'page' || backgroundAudio;
into
hasTopBarRight = (_useSearch && !moveSearchToHero) || backgroundAudio;
I know, it's a dirty hack, but it does the job for me

I noticed that if you then use the search box on a non-index-page, the search results are shown above the actual content of the page, and the content is pushed down. So I totally get why the search box isn't shown on non-index-pages. But for me, I really like a consistent navigation menu across all pages; shifting menus and dis-/reappearing icons / search boxes while a user is navigating across the site is usually a UX "no-no" according to my UX colleagues
