Are you so sure that triggering a watch dog off a signal that says "some code is running" is such a good idea? Normally the idea behind a watchdog is to try to setup the triggers of the watch dog so that you can detect that "my code is running in a reasonably expected way". Thus you embed the watch dog triggers inside the main loop of your program. It is for similar reasons why it is not useful to put watch dog triggers in a timer interrupt routine.

After all if you are just looking for an easy way to make the watch dog keep quiet so it does not reset you then just take the circuit out or disable it. In your case thebest use of the external watch dog would be to tie its trigger to a port pin that you can manage in the main body of your appliction and only then after the application has taken action to enable it. Leave the boot loader process free of need
to support the watch dog.
Mike Karas