Hotkeys (COMMAND-V …) don’t honor Dvorak layout

You can use the app Ukelele to fairly easily make a custom layout that puts the punctuation where you want it.

http://scripts.sil.org/ukelele

After making and installing a custom layout, you should be able to select it in the Kotoeri Preferences.

Apple has a patent on the autocorrect feature for mobile phones (and possibly for desktops as well). There was a lawsuit over iPhone vs Samsung autocorrect: http://gizmodo.com/5884179/apple-is-now-suing-samsung-over-autocorrect . Moving right along, apple's autocorrect does use keyboard layout to predict a replacement word: http://www.slate.com/articles/technology/technology/2010/07/yes_ill_matty_you.html . Lion will only try this feature if it can recognize the keyboard layout you are using based on a keyboard standard.