FWIW here's my observations on this very issue:
I've now installed Lion GM four times on the same machine (using identical partitions within the built-in HD).
Every time I install from within SL (from the downloaded Lion installer from App Store) I don't get this warning when installing.
However, every time I install from a DVD boot-disk (made using this method) I get this warning "Some features of Mac OSX Lion are not supported for the drive "....", such as File Vault and Recovery Mode..."
So in my case at least, it's the installation method itself that triggers this warning. From general observations, both installs for all intents and purposes are identical so it's not a real issue, at least none that I've observed.
I've now installed Lion GM four times on the same machine (using identical partitions within the built-in HD).
Every time I install from within SL (from the downloaded Lion installer from App Store) I don't get this warning when installing.
However, every time I install from a DVD boot-disk (made using this method) I get this warning "Some features of Mac OSX Lion are not supported for the drive "....", such as File Vault and Recovery Mode..."
So in my case at least, it's the installation method itself that triggers this warning. From general observations, both installs for all intents and purposes are identical so it's not a real issue, at least none that I've observed.