Thanks @isamom1982 - Not sure about state extension issues (like NY you point out) but for Federal (and states that automatically honor Federal extension), could one do the following:
1. use the desktop version to create paper form for extension but do not send it, instead,
2. Go to the irs.gov website and pay estimated tax + file for extension
This way the software is happy (it knows extension was requested) and you can still file for extension online.
