This is really the nub of it - Beane’s job gets much tougher starting now. Assuming he extends Allen within 18 months, for the next 10-15 years he’ll have to recycle the rest of the roster and play games with the cap. THAT is where good GMs distinguish themselves. Can’t afford to miss on so many draft picks and free agents when cap room becomes incredibly scarce which it is about to do. And that’s why skepticism is warranted, while Beane hit on the most important position he will, as you said, have to become more efficient with his roster decisions if they’re going to achieve sustained success. And oh by the way he’ll have to do that while losing coaches and scouts to promotions elsewhere. His journey is just beginning.
That said - extending him was the right move, and it doesn’t count under the cap so what do I care? The Pegulas have shown that they’ll eat a front office salary if expectations aren’t met.