The only problems with connecting two boards in this way will be VSWT5V0 and VCCB2 voltages - you probably don't want to share these if the boards are running from separate power supplies.
Unfortunately it also doesn't look like it's possible to power one board from another through the connector, and there aren't any jumpers that disable these voltages from appearing on the VHDCI connector. If you wanted to do some surgery you could probably remove the connector, cut the power pins, and reattach it!