Here is my maxed gear, modded JE. Showing 29.99% armor.
He has two mods that add to his defense.
If just the 11.75% defense bonus from the primary is included, about 27 armor/defense is being added to JE's maxed base of 230 = 257 armor.
If the secondary of 2.89% was also being included, the overall armor value should be about 30.49%, or another 6 defense higher. So it's about 0.5% short.
Clearly in most cases the secondaries are being taken into account correctly, but under these specific circumstances, they are not.
Ally Code 445-637-235
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