I made some measurements.
I checked the schematic via Arduino Mega 2560 - EasyEDA open source hardware lab
The signal comes out on M8RXD pin with 5Vpp. On the other pole of the resistor RN7.2 it is still present, but with 0.5Vpp only. It goes further through everything you mentioned, and returns to the RN7.1, and to the MEGA16U2 with the same 0.5Vpp voltage level.
I checked the resistor network, all elements are 1kOhm as needed, but I haven't soldered it out so there might be some problem with it. Anyway, I think the problem will be this low voltage.
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