Interesting - we obviously move in rather different circles despite being in the same business:
Take the current project:
One master processor (ARM Cortex M4 with ARM serial debugging port and 4 wire trace, Ethernet, USB and serial for debugging)
One supervisor processor (ARM Cortext M0 with ARM serial debugging port)
FPGA with JTAG port
Up to 6 slave processors (ARM Cortex M4s with ARM serial debugging ports)
All in one little box about 25cm x 160cm x 5cm
Now to bring up the Ethernet on the master processor I can use its serial port for "printf" error messages (from the Ethernet/TCP/IP library) and the ARM debugging port to load/run/trace the processor. The ARM trace interace box (Keil Ulink Pro) is a USB interface to the development PC.
The superivisor processor is connected via another Ulink to another PC.
The FPGA JTAG interface is USB to yet another PC.
The fourth PC runs Wiresharc and is connected by Ethernet to see what's coming out.
It would be nice if the debug tools had Ethernet rather than USB interfaces but they don't.
I could isolate the serial debug port but since I must have three other non-isolated connections it's not worth the effort.
This system is all quite low power - so certainly safe to humans and fairly safe to computers. (The really exposed parts are the debug interfaces and there is nothing to be done about that since they need fast conenctions to the hardware.)
In the last 10 years I've lost one debugger and one PC due to my mistakes and in the same time at least 10 PCs have just died (as they do) so it's a cost effective approach.
Of course when these things connect to external systems handling real power different rules apply.
(AFIK most Ethernet interfaces are not specifically tested for mains safety - either during qualification or as part of normal regular safety checks (and the flash test requirement for Ethernet magnetics is 1500V AC which is OK for some equipment but not for all)).