Think of it this way...
I work on rather large dialogs and custom windows when making games and other scripts and they require a lot of testing. Such testing requires going back and making changes or additions. Now, keep in mind that a lot of the scripting isn't for just initialization, so you can often leave the dialog/window open while testing. Now, in previous versions of mIRC, if I left the scripts editor in focus and switched to the dialog to test it, then switched back to mIRC, I could just start typing or scroll or search or whatever in the script. Now, I have to click on the window every single time. That's what I find annoying and I see no reason for changing the focus. If anyone sees a legitimate reason to change focus on someone, I'd be interested to hear what that is.
The on top setting doesn't solve this at all. First of all, it puts it on top of all windows, which doesn't help when you're trying to still see your dialog/window. Second, it still loses focus. The only way to prevent having to click it everytime you switch to mIRC is to have it as a desktop window, which I explained previously that I don't like.
Now, if there's a reason why it should lose focus, then okay. I'll live with it. But I really don't see any reason for the change. And if there isn't a reason, then I think it should go back to how it was.