Hi,
2.4% is a gross climb gradient the manufacturer has to demonstrate the aeroplane complies with on the 2nd segment. [and provide the conditions under which said compliance is achieved]. This is a CS/FAR 25 certification performance requirement. The 0.8 % penalty is not related to that particular performance requirement.
CS/FAR 25.115 is not refering to the 2nd segment minimum climb gradient. It's refering to obstacle clearance. ie when there is a limiting obstacle, the 35 ft clearance has to be achieved after the penalty (0.8% for twins) is applied on whatever gross gradient you have in a given case.
2.4% is a minimum gross climb gradient when there is no limiting obstacle.
0.8% is a penalty that applies when there is an obstacle to clear
I think it may be worth to cross ckeck the source of the document you posted.
Cheers
Feno