Pretty noob question, but I'm struggling to find the answer anywhere; if you're running a perk overhaul, does that mess with the perks granted to modded in followers as well? Simonrim in particular combines pickpocket with lockpick under the lockpick tree, and replaces it with a hand-to-hand perk tree, IIRC.
I don't know what all those overhauls do, so I can't answer that question.
Inigo does have the perks: AgileDevender80 and Unhindered
He might also have a few follower-specific perks that are never available to the player. I can't tell you what, if any, of those the overhaul you mentioned changes. Unless the perk overhaul does something really extreme with the perks though, the changes are unlikely to break Inigo. At worst they will make him a bit more, or a bit less, effective at a few things.
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Perk Overhaul Compatibility (2 comments)
Inigo does have the perks:
AgileDevender80 and
Unhindered
He might also have a few follower-specific perks that are never available to the player. I can't tell you what, if any, of those the overhaul you mentioned changes. Unless the perk overhaul does something really extreme with the perks though, the changes are unlikely to break Inigo. At worst they will make him a bit more, or a bit less, effective at a few things.