1. Lossy codecs will use a low-pass filter to get rid of hard to compress higher frequencies. This is often inaudible, but even when it is, it should lower the volume, unless you're applying some kind of compensation for it.
2. It's true that lossy codecs compress different frequencies differently, but that's not usually done in such a way that amounts to applying EQ to the frequencies.
3. Even if the relative balance of frequencies did shift as a result of applying lossy compression, this is still done in a way that the overall loudness of the audio does not change. In this case the Lyra output has changed significantly and in an easily audible way (about +6 dB). You could easily get the same effect in Opus just by amplifying (or applying compression to) the result, but Opus is doing things correctly.
I guess that can be tweaked either way but they're going to tend towards that exactly because it sounds louder and thus clearer.