The authors of this script have been really slack in not removing those calls before allowing their script to go live.
We have made alerts the part of miniBB's interface. It's the simplest approach to report user something. It comes in a modal window and can't be just closed, and it doesn't require jQuery or similar libraries, which size is bigger than miniBB's package. It just few bytes of code, so we're happy to live with it. It's truly visible. The approach you mention above (div/innerHTML) is not that visible and can be simply ignored.
Are you coming from the brontosaurus
I can as all here to wait while forum's author decide to change this behavior of forum
You risk to wait forever. We have no plans to change behaviours of thousands of people just because of two opinions.
A div in the form with an id and then using innerHTML to update the content of the div with the error message has been the standard way of producing error messages on forms for the last eight or so years.
Could you please point us to the article or document, which clarifies such kind of standard and proofs it's a "standard way"? I personally never read about that.
Each project is being developed using approaches which fit it best.
Guys, it's very simple to criticize something just because you don't like it. How about offering more practical approach? It's open source. Take it, modify it and re-submit to miniBB project. Then it will be your participance. Until that, you all just sound empty.