"Lossy" refers to how digital files are stored. The format. Lossy file formats process the digital data and *intentionally* REMOVE some of the data. That data is thrown away. This makes the resulting file smaller than the raw data. MP3, AAC, and other formats are lossy.
Lossless formats (like FLAC and ALAC) do not throw away ANY data. They have all of the data.
Now, when you play back any of these formats with MC and apply EQ, the resulting data is changed from the original. This process is not the same as "lossy compression" that is applied to MP3s. It's just a digital transformation that changes the sound, in a non-lossy way.
Any time you apply EQ, you are changing the sound data; maybe in a good way, maybe in a bad way. There's no concept of "part of the sound" being bit perfect. Either you change it with EQ or you don't change it. As soon as you apply any kind of EQ, volume change, etc, the entire bandwidth of the data is changed and is no longer bit perfect.
So, apply EQ and see if you like it. You can always turn it off if you don't.
Brian.