FYI: Your perk changes override the non-perk fixes made by the Unofficial Skyrim Patch and Unofficial Dragonborn Patch. For anyone using these patches, which should be everyone by now, you'll need to use TES5Edit to copy over the USKP and UDGP changes. It's a painless drag-and-drop process but there are a good number of NPC records to update.
It ALSO messes up things like EEO and Bijin for the characters if it ends up in your bashed patch, which it will, or if it is below these mods in the mod order.
An easier solution would be to edit the follower in the CK and check the box by "Does not affect stealth meter". That way no follower that you use, stealthy or otherwise, will affect stealth. Now granted it's not "lore-friendly" doing it this way, so if you like realism, this probably isn't the way to go. But if you just want it so that they don't get detected, this is probably the easier, and more compatible way to do it. I haven't actually tested it yet with a stealth character, as I am not playing one atm. But all of the follower mods I have made, all use the "does not affect stealth meter", and I haven't had any reports that it wasn't working.
But don't take my comment the wrong way, this is still a nice mod. And like I said, I haven't had a chance to test it with a stealth character yet, so I don't know if followers can even do stealth kills with just that box checked.
Actually, I think what the "does not affect stealth meter" setting does is that it makes it so that the stealth "eye" does not react when the follower detects the player. This is generally used on non-hostile animals and followers because otherwise it would be impossible for the player to determine whether they were detected by the enemy or simply by the follower who was right behind them. I don't believe that it has any effect on whether or not the enemy can detect the follower.
I also thought that "does not affect stealth meter", was the setting that determined if you were still considered hidden if the actor could see you. I believe there is a mod which adds this effect to horses as they do not react to hidden characters regardless of faction, so you can tell if your hidden to enemies or not when sneaking near yours or an enemy horse.
According to http://www.creationkit.com/Category:Actor checking the " Doesn't affect stealth meter" is used so " When this actor detects the player, the stealth meter does not react. Typically used for non-hostile actors such as foxes, rabbits, deer, etc."
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But don't take my comment the wrong way, this is still a nice mod. And like I said, I haven't had a chance to test it with a stealth character yet, so I don't know if followers can even do stealth kills with just that box checked.