Theo Compensation Settled? Results very unsettling

When it was made known that the Cubs and Red Sox had to settle what the compensation would be for the Red Sox to allow Theo Epstein to scoot out of Boston after their incredible collapse, it was quite apparent that Boston didn't want to just give Theo away for anything.

Rumors swirled, outlandish ideas of Castro or Garza going to Boston were made. However, it was known that Boston's upper-management believed Theo was worth far more than even Theo believed he was worth. Was it "sour grapes" on Larry or John's behalf that their boy-genius savior left town after too much turmoil on what was the cause of Boston's historic September collapse?

Theo joined the Cubs, without compensation being settled.

A full month went on, no settlement.

Bud Selig gave both teams a deadline before he'd step in and settle the compensation himself....again, no settlement. However, both teams were given an extension of a undetermined length.

Time passed, both teams went on with their off-seasons without even a whisper of compensation. Finally both sides raised their hands and sent the order to Selig to let the MLB offices settle the compensation dispute.

A month passed, since then, and Pitchers & Catchers reported.....Compensation Settled....

Now, I'm just a fan of baseball who dabbles in prospects but knows generally about most major leaguers to some extent. However, why did it take almost 4 months to figure out that pitching prospect Chris Carpenter and an exchanging of PTBNLs of little-to-no-consequence would be the overall compensation?

Also, why is Boston forced to send a PTBNL to the Cubs when they were hornswaggled by the Cubs in allowing Epstein to be hired before they were compensated for letting him go before his contract expired?

Some Cub fans will point out that they think it's unjust that Carpenter was the player dealt and not a lower-level prospect(Junior Lake or Josh Vitters) and how the PTBNLs on both sides will be "organizational" filler. However, Organizational filler for a winning team with a strong farm system is vastly different than a team who's farm is "okay" and the franchise is being totally re-done. One man's trash is another man's treasure.