Your missing my particular context. In an intrigue campaign, you're putting additional emphasis on skills, and you are going to tend to have parties with more homogeneous skills sets as a whole (deception, investigation, stealth etc). That one character isn't niche anymore, and his massive skill check takes away any real interest other party members are going to have in using that skill. It also makes it difficult to build narrative tension by providing appropriate challenges."Party balance" in what sense? Why is it bad that this character can do a thing well and others can't? Wouldn't it be the case that this expert won't be able to do other things as well in this or the other two pillars?
Also, how is "deception in the hands of a creative player" troublesome? Setting aside that the DM decides whether there is a roll or not in the first place, what's the actual trouble here? That the NPCs get messed with? Because, if so, that's kind of what the characters do, right?
Example one: Lets say the party is going to infiltrate the Duke's ball in disguise. I can't provide an NPC with appropriate skill levels for opposed rolls. Either our superhero is always good and everyone else has an appropriately tense time, or that NPC essentially auto-spots anyone but the superhero. This has several obvious side effects on a campaign, none of which I enjoy.
Example two: The party is approached by the city watch and decides to talk their way out of trouble. Several characters have good CHA and deception, but the only character who is ever actually going to make that roll is the one with expertise. There's just too big a gap for anything else to make sense, even though it really cuts in on the fun of players who built solid non-rogue characters with the right skill set for the campaign. There isn't even a compelling reason to use a spell for the same job, since the spell is a finite resource and the skill isn't
The troublesome part comes back to mods and the comparison to the rest of the party, plus the nature of opposed rolls in the system. A creative player will essentially auto deceive anyone he meets, and you can't challenge them without making it impossible for the rest of the party to succeed at the same task. Anyway, I get that my problems with this are kind of niche based on the kind of campaign I'm using for context.