Does Turbotax Canada handle the additional forms required for filing a final estate tax return? If yes what version of the software should I be using?

TurboTax can't do a  T3 Trust Income Tax and Information Return. However, Intuit has another product called Profile which does have the ability to to T3 returns. You can read about it here: https://profile.intuit.ca/profile-onepay/

Please be aware that Profile uses EFILE to file online, not NETFILE. EFILE requires you to register with the CRA. You also have the option to print & mail your return.