Yes, the second mirc has the mirc.ini in the folder of it's mirc.exe.
I have restarted it still read the mirc.ini from the AppData.
Here are the result of the command:

C:\Program Files\BotScript\mirc.exe uses C:\Users\ΑΝΤΩΝΙΟΣ\AppData\Roaming\mIRC\mirc.ini

I have put the mirc.ini into C:\Program Files\BotScript\mirc.exe