I'm not sure you understand exactly what root does. Root gives you "root" level access, aka Superuser, aka Administrator access. Think of Android like a computer in a public library. Lots of things (settings, certain programs, certain directories mainly) are locked down and inaccessible by people who don't have the password or an admin account, because they don't want people messing around with them. Android is the same way. Many (most?) people think of smartphones as just that - phones. They don't think of it as a computer, even though that's exactly what it is, in every aspect of the word. Without restrictions, it would be very, very easy for the average user to completely screw up their phone.
And that is why Android comes with these restrictions (which carriers exploit to install unremovable apps). Rooting your phone removes many of these restrictions, which is also why rooting typically voids your warranty. You might want to root to get rid of useless bloatware like NFL Mobile or Verizon Navigation or Samsung's browser because you only use Chrome. But it's just as easy to (accidentally or stupidly) delete a core Android program, and now your phone is stuck in a crash loop and you've got a $700 battery powered paper weight.
That said, root gives you Superuser access. And that's it. Root doesn't change anything, for better or worse.
It's what you do with that access that matters. Freezing/deleting bloatware that would otherwise be constantly running in the background can improve your phone's performance. You can install the Xposed framework to clear up your notification panel and status bar, add functionality to your buttons, and port features from other brands to work on yours. Tasker is a very powerful (and very confusing) app that you can use to make your phone do things automatically depending on where you are, when it is, etc. You can block ads within games and browsers. You can do back-ups of your apps and data and share them between devices, or when moving from and old phone to a new one. With root sometimes you can bypass restrictions imposed by the carrier because they want to milk you for more money (like wifi hotspot).
I'm also not certain you understand what a launcher is. The launcher is merely the interface. Homescreens, app drawer, dock, icons, etc. I honestly don't know what a 3rd party launcher like Nova, Apex, or Go does to S-Pen functionality on the Note series. But it's merely a different interface, which can be disabled or uninstalled without issue.
What you might be thinking of is the ROM itself. ROM is a bit of a misnomer (meaning Read Only Memory, like a CD_ROM or DVD-ROM), but in the Android world, the ROM is what we have taken to call the operating system. For example, a TouchWiz ROM is heavily modified, and very different than the ROM of a Nexus, which is 100% "stock" Android. Then you have custom ROMs like Cyanogenmod. Installing a different ROM on your Note 4 will absolutely kill your S-Pen functionality, unless it's based on the stock N4 ROM (for example, stock, but debloated, streamlined, and tweaked a bit) and retains those features that Samsung built into it.
With a launcher you can make one phone's homescreen and app drawer look like another's. But when you go into the settings, they'll look different, because that's the ROM, not the launcher you're looking at.
One thing to nota bene is that Samsung has become increasingly restrictive about root and unlocked bootloaders. An unlocked bootloader is required to flash a different ROM (although running different ROMs in Safestrap is usually still possible). Samsung flagships from AT&T and Verizon are notoriously restricted. Google "towelroot" to find out just how restrictive they're getting. Of the "big 4" US carriers, T-Mobile is undoubtedly the least restrictive. With AT&T and T-Mo you also have the option to buy an "unlocked" device, but you won't get the pay-over-time benefits of a subsidy or payment plan. "Unlocked" refers to carrier compatibility, not the bootloader (although carrier unlocked phones are typically easier to unlock the bootloader). But if you subsidize a phone from VZW or AT&T, particularly one from the Samsung Note or Galaxy S line, it's entirely possible that root might never be achieved, or might take a long time. We're talking about rooting a phone that isn't even out yet, and we have no idea what kind of "security" measures are in store.
Root is a powerful tool, but the most powerful tool for your phone other than root is knowledge. Read, read, read, read, ask some questions, and read and read. Find some "for dummies" guides and read those. Watch some youtube videos. The problem with XDA, if there is one, is that stuff like this doesn't have a learning "curve" so much as a learning "sheer cliff made of buttered ice". Lots of acronyms, jargon, technical terms, and other gibberish. Grab some coffee or Red Bull, and start learning.
Relax, go nutz!