9% nerf to pokemon over 4000 CP explanation?

I'm no expert and haven't bothered looking up stats, but I believe what's missing from your question is:
Defense: is actually 5/8 better and 3/8 worse out of defense and special defense stats in the main games. Perhaps this explains the difference?
Stamina: not sure on the conversion formula but there was a change to reduce it by a certain percentage and add a flat amount. I think the regular games had a flat amount too though, so I'm not sure.

My understanding was that each stat was nerfed by 9% though.

Groudon's stats prenerf are 297 / 250 / 225

Stamina: 1.75*100+50 = 225
Defense: Round(Round(2*(5/8*140)+(3/8*90))*SpeedMod))= 250
Speed Mod: 1+((90-75)/500) = 1.03

Multiply them by 0.91 and you get the current results.

Groudon's main series base stats:

HP: 100
Attack: 150
Defense: 140
Sp.Attack: 100
Sp.Defense: 90
Speed: 90

Speedmod = 1 + (90-75)/500 = 1.03

ScaledDefense = Round(2(5/8 * 140 + 3/8 * 90)) = 243
Defense = Round(243 * 1.03) = 250
9% Nerf = Round(250 * 0.91) = 228

Stamina = Floor(100 * 1.75 + 50) = 225
9% Nerf = Round(225 * 0.91) = 205

I'm not sure where you're getting 276/251 from for its original stats but my math adds up to its current stats. Maybe you're looking at old formulas?