Chuck,
I'm not an engineer, but I've worked with one on special problems and special builds for the last 9 years. I've seen this done several times (or something similar). I've worked with building/repairing roof trusses, modifying trusses, beam trusses, floor trusses (open web joists), and TJI's.
The only reason I can see that they don't want to do this is the added cost of the build, engineering change, and approval, for carrying a short beam, or double 2x6/8 etc depending on span of the short truss and adjacent trusses.
You should be able to give dimensions and idea to the engineer and should be no problem. 2 double hangers for the header and basically a modified jack truss and your in business! Just get the engineer to build the bottom cord the way
you want it to save on all the blocking for sheet rock etc if that's a concern. Some of the guys I've dealt with just seem to forget that the truss does a little more than just support a roof load (like making it easier to have the sheetrock look flat on the transition of 30' trusses,built with camber, to a girder, built with no camber, to short trusses on a popout with 1" of camber!!
) Well, it looked good on the computer I'm sure!
If you lived in washington I could give you the name of an excelent engineer...