The Mega has too much memory to run a bootloader that speaks STK500V1. You need an STK500V2 bootloader.
How long a WDT interval do you need? As long as the bootloader gives control to setup() before the WDT times out again you should not have a problem with the bootloader.
Have you tried the WDT with the standard bootloader?
Here is a WDT test sketch. It blinks slower and slower until the toggle delay grows beyond the WDT limit. At that point the WDT times out and resets the system.
unsigned long ToggleDelay;
const int LEDpin = 13;
ToggleDelay = 1;
wdt_enable(WDTO_250MS); // Set watchdog to 1/4 second
ToggleDelay += 5;