Can a Mega reset pin be controlled with code?

But maybe not long enough.
I definitely remember that there were some issues related to watchdog in the early bootloaders like back in the 2010 and earlier time frame.

I have a note in some old sketch code of mine for the atmega168 from back in early 2011 that says:
If you did a watchdog reset when using an old bootloader that the board would go into a reset/boot loop until it was power cycled.

I'm sure if we really wanted to we could dig deep enough into the git history of the original "MEGA" bootloader, optiboot, and forum posts we could find out what the issue was and when it was fixed.

These days, I'm assuming that users will have a new enough bootloader, particularly if using optiboot in their board that they will not see the issue.

What makes things messy / complicated is that there are multiple bootloaders that have conditionals so that they can be built in multiple ways and some of them may still have the issue. So depending on which board you have, you may see the issue.
i.e. not all Arduino boards are using optiboot.

From a quick look in forum posts, it looks like there are still some issues on some boards.

--- bill