Think it as zipping a whatever file: you can choose the amount of compression, that won't alter the file content.
Similar for FLAC, depending on the algorithm used, the spectral content will be the same, though you can't really think it as just a container.

However, to be sure, do this experiment: rip a CD wav file, flac it, then re-convert it again to wav and then null it in daw with the original one (or file compare it for extreme testing) and check with a spectrum analyzer, you basically should not have any spurious frequencies (no strange peaks above -100dB).

BTW, if flac was really different, the term "lossless" would be not suitable, should be "almost".

FTF is an awesome tool, however it just checks that audio content spectrum reaches the maximum frequency band cababilities of the used codec.
If, for example, you generate 500Hz file and save it as wav (as you know uncompressed), it will say that is a fake file.
Here the above test of spectrograms of a 440Hz coded in pure wav file at 16 bits and 48k, 44.1k, 22k and 11k Hz.
As expected, all 4 pure wav files were considered fake, something that is not.

 

Last edited: May 5, 2024

Are you sure about the source file being the same? Otherwise, two flacs of course can be different. Unless you converted them yourself you probably have no idea whether they were created using the same source file.