I understand your concern, if this is a bug, then you could request a refund and there is no charge for bugs.
Please understand I could not confirm this is a bug  or not because it is beyond my authority.

I agree with you on the following factors:
1) Setting the Pages library  to not require  checkout is a valid and legal operation
2) Creating a variation  hierarchy is a valid and legal operation
However, I am not sure whether it is true that “3) Operations 1) and 2) are independent and unrelated operations”.
That is why I suggest you to contact premier support, and they could help you to check the internal  logic then give you a proper answer  which I can’t.

Based on my understanding, Variations use in planning phrase. During the planning, I seldom change the SharePoint settings. If possible, I would like to ask you to create  you custom  solution based on default SharePoint settings.

Last but not the least, in connect.microsoft.com, you could submit  your feedback at:
https://connect.microsoft.com/feedback/default.aspx?SiteID=428