I talked to support @ AJA and they confirmed that all of the SDI and HDMI ports on the box are just pass throughs.
3GB might need higher grade cables between the box and the card, but the internal jumpers are probably too short to be trouble. If they seem to causing a loss, the high grade 3G cables could be plugged directly into the card. And you would need to bend down and plug HDMI cables into the card directly.
Support didn't know if the Control Panel would identify the box correctly, but said it's all the same pin-outs, so it shouldn't hurt anything to try.
Control Panel does still identify the system as LHi and appears to have full control.
Of course I don't have the real box to compare, so something might be missing, but all screens in the manual show up in control panel.
I will report back if the fire department has to visit.