The ability and equipment shuffles of version 1.11 add a LOT of complexity to the game. Surprisingly good and singularly terrible characters are both fairly common, so be ready to dual wield some Power Staves on an Edward and expect him to carry your team if that's what the situation calls for! On average, you should expect a seed with these options enabled to be harder to complete, both because it is more confusing and because it is more common to have a weak party in some portion of the game.
Details on how corner cases like Rydia's aging are handled can be found in the Change Log in the Documentation folder.
In other news, The Lunarian Shuffle now has a proper installer instead of being a standalone .exe. This should make it easier to use for those who were having trouble with overly aggressive antivirus settings giving it a false positive.
The download location remains unchanged:
However, now you will be downloading and unpacking a .zip file containing the installer.