Mesa RPI4 Ethernet vs GPIO?

Any pros / cons for using a mesa Ethernet board like the 7I96 vs using the 7C81 with a 7I78 for a Raspberry Pi? Tried reading around and couldn't find any comparisons, only "not to use a switch" if going the Ethernet route...

The ethernet boards are easily transferred to another platform, with the RPi specific boards you are limited to the RPi. Something to think about for the future.
The ethernet boards can be put in a cabinet\enclosure separate from RPi or PC.
These are just my thoughts.

you shoudt consider the slightly higher cost on mini-Atx but gives you so mutch advantige on use

Platform agnostic is a good point... wouldn't have thought about that, so thank you!

The pi is used mainly as an interface, like octoprint for a reprap printer, so I don't think the mini-atx would give me much benefit

You understand that Linuxcnc still calculates all the motion control, regardless of what board you use. The MESA boards do the timing but not the GCode interpretation. So no the RPi would not be used mainly as an interface,it's an integral part of Linuxcnc.
I hope you weren't under the assumption that Linuxcnc is a glorified gcode sender, similar to gerbl ? The PC or SBC that runs Linuxcnc is the CNC controller.

You would gain benefit from a modern x86 platform, greater amount of memory, ability to use a SSD closer to it's native speed with a SATA interface rather than USB3 to SATA.