I see what could be the issue but I do not understand one aspect though:
how could we switch from one PHY to another, as there's only one output
between the SoC (and so a given GoP#) and the board. So if a given PHY
can handle multiple modes I see, but in the other case a muxing
somewhere would be needed? Or did I miss something?

I think we need a hardware diagram...

How are the RJ45, copper PHY, SFP module connected to the SoC?

Somewhere there must be a mux, to select between copper and
fibre. Where is that mux?

    Andrew