I see what you mean about the buttons moving around, via the dialog box changing size as the file pathname greatly changes in length from file to file. I haven’t looked at the source code, but it is probably done with a standard Windows YES-NO-CANCEL MessageBox call, in which case I totally understand this behavior.
I’m not sure how much you prefer mouse versus keyboard, but as a workaround, how about just pressing the N (or Y, in case you need that…) key when that dialog box appears? (Alt+N or Alt+Y also work, but that just seems like unnecessary extra effort.)
I totally understand if you know about the keyboard possibility and are just making a feature request. However, the right people either won’t see it here, and/or aren’t going to track it here.
Your best option is to make a feature request or a change-in-functionality request here. Please spend a little time searching to see if your specific request already exists (in which case you can “up-vote” that request, and/or add any new information you think relevant).
If this (or ANY other posting on the Notepad++ Community site) is useful, don’t reply with a “thanks”, simply up-vote ( click the ^ in the ^ 0 v area on the right ).