There is a work-around you can use to achieve this: you can connect a zone wire simultaneously to two zone ports on OpenSprinkler (either by splitting the wire, or by connecting two wires to the same zone wire). That way, you have two zones (say, zones 1 and 7) actually controlling the same physical valve. You can leave one of them (say Zone 1) in sequential mode, and the other zone (say 7), in parallel (non-sequential) mode. This way, either zone 1 or 7 can turn on that physical zone, but zone 1 will be used in sequential programs, and zone 7 will be used in parallel programs.
The only downside of this is that it requires twice as many zones as the number of physical zones. But expanders are relatively cheap so it shouldn’t be a huge issue.
Creating independent groups is on the firmware todo list, but it’s not a trivial thing to implement and it requires changing the user interface considerably.