Hello karthick,
The GT16A is an improved GT16 and a GT16 is a cutdown GB60.
The GB60 had a 3 and 5 channel TPM. Only the 64-pin package bonded all of the pins out though.
The GT16 had the same TPM but the biggest package only bonded out the first three then two of the second one.
The other three were there and you could use them for other internal purposes.
The GT16A was designed from the "ground up" and it does only have a three and two channel TPM. This fact is not properly dealt with in the manual and was absent completely from EB671 which was supposed to help you with migration from non-A to A (as long as you were only using the stuff they bothered to cover)
The mentions of the old three plus five channel TPM is a relic from the GT16/GB60 and is wrong. This has been pointed out on several occasions here but nobody has bothered to fix the documentation. If you like you can do an advanced search for posts by me with GT16 and GT16A in them to see the history.
The GT16A/8A glossy fact sheet when the device was released only advertised a 3+2 TPM.
In your case one pin is not bonded out, it is still there, just not externally accessible.
You have to be wary when using the lower pin count packages that you are properly handling the unbonded pins.