White's intended setup involves fianchettoing his dark-squared bishop on b2. The "free move" 6. Bd2 brings more harm than good:
Transferring the bishop onto the long diagonal, if white wishes to, will still take another move (i.e. Bd2-c3), but more importantly, if he does, the bishop on c3 takes away the square for the knight, which is preferred in many lines.
In many lines, white wants to play d5, aiming for a Benoni-like structure (which is bad for black in these cases); the bishop on d2 blocks the queen's defence of the d5 square, making this push harder to achieve.
For case 1: consider the "old" line, and compare this to a possible variation that arises after giving the check on move 5 instead:
1. d4 Nf6 2. c4 e6 3. Nf3 b6 4. g3 (4... Ba6 5. b3 Bb4+ 6. Bd2 Be7 7. Bg2 Bb7 8. O-O O-O 9. Nc3) Bb7 5. Bg2 Be7 6. O-O O-O 7. Nc3 Ne4 8. Qc2 Nxc3 9. Qxc3 f5 10. b3 Bf6 11. Bb2
Clearly, in this case, having the bishop on d2 is worse than having it on c1!
Long story short: the check disrupts white's set-up.