Hello,
I am not sure how you check the SWT but by default is it set:

Not sure what represents your IRQ handler as this device has 2 SWT (SWT_A and SWT_B).
In your IRQ, do you see the TIF flag for SWT set on module A or B?
Then how come this SWT1 ISR is executing not clear for me. Is this ISR used for some other exceptions?
Because your SWT is enabled and has expired. No big magic here. HW will set TIF flag, which will trigger IVOR4, where the offset points to SWT interrupt.
If the SWT is not enabled, TIF is not set, and no IVOR4 is called.
Debugging SWT is tricky as as soon as you attached debugger will disable it. So you will see WEN =0.
You better use SW to store the SWT CR register value in ISR when it is called and read that variable by debugger.
Best regards,
Peter