Signal ground and power ground

You can manually add a net using Design->Netlist->Edit nets, then select each pad and assign that net to it.

But I don't see why you don't want to do this in the schematic.

There could be a risk from ground "fault" currents. You haven't mentioned how far apart these power supplies are and what else their individual grounds may be connected to. In an industrial environment, for instance, a ground fault current on machine X may cause excessive currents to pass thru the grounds of other pieces of equipment. This may give rise to secondary failure of connected devices. It may also give rise to intermittent or faulty operation of other devices too.

On the other hand, if you have AC powered supplies and they are isolated on their respective outputs, there is little chance of problems when connecting grounds.