Update: October 29, 2010 There is one more difference – More information about Family Tree Maker 2010 for Mac.
The $99.95 version at Amazon.com, Amazon.co.uk, etc. has the “Family History Toolkit” which is a collection of ebooks on a DVD. There is no difference in the software between the Ancestry.com and Amazon.com versions!
The short (and long) answer is it’s simply a matter of an Ancestry.com subscription.
The retail version, such as what we see at Amazon.com which normally runs $99.55, as well as the retail version in the UK such as Amazon.co.uk (United Kingdom) which is normally £59.99 (on sale for £46.99) includes a 6-month subscription to Ancestry.com. The Ancestry.com version linked above does not have this subscription and sells for $69.95. It makes perfect sense from that perspective.
I do have more questions submitted to the folks behind FTM and will post the responses as I get them. I am slowly but surely working through the back-log of questions I’ve received from people who follow this site, and will get them answered and posted either in a new article, or through the Frequently Asked Questions (FAQ) as time permits. If you’ve asked me a question through the contact form or directly through email, rest assured you will get a response soon. I’ve answered probably 50 emails in the past week alone.
If you have a question, please send me a note through the contact form and I’ll get you a response.