... except when mIRC needs to update the servers
That one specific endeavor is a huge deal and needs to take center stage high priority. It's not a mere whimsy activity.
How can a user update their servers if they also have 20 custom servers they've since added and edited of their own?
There is no merge or migrate feature, yet, and so it should be done that the two lists be made separate. Just like your spell check dictionary in every platform.
If some nimrod wrote a script that manually parses the default servers.ini file, and can't be bothered to update their script, then they should continue using a singular servers.ini file. The rest of us don't care about that nimrod.