How can I add or activate tools (extensions) like graph, math, and etc to the standalone version?
Topic on Talk:VisualEditor
The stand-alone (non-MediaWiki) version of VisualEditor can be extended by writing code along the lines of VisualEditor/Gadgets#Triggering a command using a toolbar tool (though some of the advice there will not apply, because it's talking about the MediaWiki context).
The MediaWiki extensions you mention are each reliant on MediaWiki, and so can't be added to the stand-alone version of VisualEditor.