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This should be fixed in the current dev build, at If you could give it a go and confirm for me, that'd be great.
You can use view.sel().add(sublime.Region(x, y)) to add a region to the selection. The functions on the selection ('RegionSet'), haven't changed apart from case from Sublime Text 1, so you can reference the API docs for the other functions on view.sel().

In this case though, you may be better off using view.replace(region, string), which will replace the region, but preserve any selection at that region.
The setting is getting overridden by the Python specific one. If you make a new file User/Python.sublime-settings, and place your word wrap setting in there, then it should apply.
This was added in the latest version
Added for OS X in build 2020
OS X Save As key binding has been added in build 2020