Hi,
I tested watchdog in STOP mode and it works correct on my side. I created simple example, which demonstrates the functionality of STP bit in SWT_CR register.
Please see example and also Reset signal. In my example I defined macro STOP_SWT. If this symbol is set to 1, watchdog is stopped in STOP mode, if STOP_SWT is 0, watchdog is running in STOP mode. I tested the example without debugger connected.
First case: SWT is disabled in STOP mode:
1) Reset signal after power on reset

2) Reset signal when microcontroller is running

Second case: SWT is enabled in STOP mode:
1) Reset signal after power on reset

2) Reset signal when microcontroller is running

In the first case you see, there is no reset, because SWT is stopped while microcontroller is in STOP mode (I do not wake up micro from STOP mode in my example).
In the second case there is periodical reset caused by SWT, because SWT is still running, even if microcontroller is in STOP mode.
Please test the example, and let me know if it works on your side.
PS: I did not test your example, but if I were you, I will check the STOP mode at first. Because if there is some pending interrupt or some event, microcontroller does not go to STOP mode and STP bit in SWT has no effect. It is also better to test the example without debugger.
I use MPC5744P 1N15P, so we have the same mask.
Regards,
Martin