He operates in a silo of cap management. He does not treat the salary cap management for the imaginary plaything that it is.
In fact a lot of the shitty cap management issues we had until we finally fucking figured it out were on, guess who?
This is the crux of things to me. His degree is in engineering, he doesn't have the same ability to bullshit/socially manipulate people and situations as Jerry, I think he's pretty pragmatic and calculating even if not extremely intelligent, and I think he cocooned himself in the financials/cap aspect of the football operation when he came on 30 years ago or whatever.
There's a reason he's the guy who was "putting Jerry against a wall" over the Deion contract when he was like 28 or whatever.
In lieu of actually being a legitimate football mind who can dynamically and creatively adjust and respond to evolving circumstances, evaluate talent and so forth, he's chosen to wrap himself in the cap stuff and has elevated it's importance (whether consciously or subconsciously) by seemingly creating these rigid standards by which they allocate cap space and make decisions on players.
I'll give him some credit for the draft stuff, we've been pretty great there and it's really been the only saving grace over the last 10 or so years, but Stephen definitely strikes me as a bean counter who has chosen to kind of mold the organization around that piece of the football operation because that's what he thinks he's good at.
I'm not sure what you mean about the "Jones" brand, he doesn't seem to play up the nonsense the same way as Jerry does, unless you mean he knows he has to keep Jerry comfortable and feeling like he's in power.