The noise cancellation mic being covered or not should have no effect on the clarity of the primary mic. What SHOULD happen if the NC mic is covered, is that you just lose your noise cancellation feature. I just tested it on an iPhone 5C and an HTC M8 (both ways), and there was no difference in clarity with the NC mic covered or uncovered. Either your particular phone is defective, or they designed it wrong.
I think it does have an effect. My call recipients have no problem hearing me at all when I hold the phone to my face or place it on a desk in speakerphone. So either the OP is freakishly unlucky with defective replacements or he's really covering that NC mic up. My thinking is that they designed it in such a way that totally covering it up has ill effects for certain people's usage. That's not a defect though, it's a design decision that affects certain people. If your particular usage compels you to cause that problem you could solve it with a BT headset or look for another brand that doesn't affect call quality when you shoulder it.