I'd just like to say that everything in this post is wrong. From the math all the way down to what is actually being said.
First off, 25% of 125 is not 25. Its 31.25.
Secondly, if that were true, you would be getting over 1200 exp per lvl 50 mob. Last I checked, you don't. What actually happens is that you and your chocobo both get 100% exp from the kill. The exp that goes to your character is then given whatever exp bonuses you have at the time(rested bonus, fc buff bonus, etc). The chocobo however, does benefit from the chain exp bonus.
Just to repeat myself, the chocobo DOES NOT steal your exp.
EDIT: Also just to add on to this, your chocobo will not get any experience if your level is too high. So if you wouldn't normally get exp from the mob, your chocobo won't get any. The only exception to this is when you're at 50 at which point only high level mobs will give your chocobo exp. I don't know the exact levels that you can get exp from but generally you want to kill 49/50 mobs.