Tone.cpp indeed has the same warning.
The necessary changes to the Tone file have been documented. You could search for the fix, and implement it.
Is there a way to workaround this? Ideally I prefer to get Zero warnings.
See above. There are plenty of other warnings that are not shown to you, so zero warnings is pretty difficult to achieve.
Why is the the usage of F() strings recommended if the compiler warns against it??
The F() macro moves strings into program memory, removing them from SRAM, making SRAM available for other things. The compiler isn't warning against using F() in general, only in what Tone specifically is doing that causes the issue.