Yes the letters do matter, if you actually want to communicate effectively. Everyone can intuitively understand what "A, B, C" means. No one would have a clue what "Apple, Orange, Banana" means. So using "Apple, Orange, Banana" to mean the same thing, when you could have used "A, B, C", automatically makes your tier list a worse communication tool.
A break in natural language order should have specific meaning, not random. Use S to say "These characters don't fall in the natural order with everyone else. They're not A, they're not A+, they're something else entirely." That's a good use of S. But using "S, A, B" to mean the same thing as "A, B, C" (for... reasons??) automatically makes your tier list a worse communication tool.
One of the reasons tier lists are useless is exactly because creators just make up their own rules every time. You're never really sure what you're looking at. If we actually did have consistent, agreed-on rules creators would stick to, we could compare and aggregate lists and they might actually communicate useful information.
As is, tier lists are just clickbait that creators throw up for cheap views (because they know people love to talk about them, even though we all know they're useless clickbait... what does that say about us??)