That exactly is the reason, why I am proposing this patch!
If you change variants.cpp by commenting out the WDT_disable(WDT); line, you break the core libraries for many other programs, as the watchdog is always active
If you do that, you have to edit variants.cpp for each program, depending if you need watchdog in your program or not.
The other way would be copying all the files to a second board, how it is done for the DigiX. But that needs twice the space on disk and constant sync of both directories for new versions of the IDE. VERY BAD!!
That exactly was the situation, where I came to the solution for my patch!
Read the entry post of that thread! I replace the line you are disabling with a line calling a new weak function WDT_Initialze(). This function does primarly the same, as the current line and is disabling WDT.
HOWEVER: A weak function can be redefined somewhere through a strong version. When the linker finds a function with the same name, this function will be used instead of the weak one.
That means: Once my patch is included in the CORE files nothing changes at all, as reset is still disabled. So we are backwards compatible.
But as soon, as you are creating a STRONG function WDT_Initialze() in your code, which will call WDT_Enable() instead of WDT_Disable() you can use WDT, where you need.
This workaround is needed, as the ARDUINO-architecture gives you no way, to influence main() before setup() is called.