So you mean I should test what happens without the transformer? I never thought about that, but it is indeed not really necessary here. There source is transformer balanced and the receiver chip (MAX3280E) has A-B inputs (no ground connection).
Interestingly, the DA side uses the exact same transformers and has the same caps on the outputs. As have the analog inputs and outputs. That's why I'm starting to think it was just as a safety precaution against RF on all fronts (and backs).
The receiver chip doesn't remove any jitter and there is no traditional PLL: "The DAC uses a low jitter digital controlled oscillator (SiLabs si570), data is sent though a short FIFO and the FPGA and uC work together to measure incoming bitrate and adjust clock as needed, basically a digital PLL with very fast lock and very slow filtering."
In theory it should put out a perfect 0.8 ps clock signal to the DAC, but there are all kinds of differences audible depending on the source. I can point you to a very long thread about that converter if you are interested, other people are hearing these differences, too.