The game doesn't layer bonuses, it uses addition over multiplication.

Take health, for example. On normal you get +15%, glass cannon you get -50%, lone wolf you get 70%.
In total, you'd have 100% health plus 15 - 50 + 70 or a total of 135%, because the game takes your base, smooshes the other numbers together, then does a little dance and makes the sum.

For armor - armor specialist and thick skin are both added at the same time.
So with a base armor of 20, thick skin, man at arms and armor spec of 1 you'd see the following:
A regular guy has 20 armor
You get the 5% bonus on top of this, which is worth 1 more.
You get thick skin which is worth 5 + twice man at arms rating, so 7.
You smoosh it all together to get 20+1+7 or 28. You wouldn't get a 5% of the thick skin because nothing in the game has shown anywhere it layers bonuses, it just smooshes them together.

Obviously you'll wait for official response because you want to hope it's an error, but it's not. They don't layer bonuses.