You should be able to do this.
There is no reason you cannot mix aspect ratios on a DVD, and Encore is an abstraction layer tool so it will automatically put the 4:3 footage into a different VTS than the 16:9 footage - Are you certain Encore cannot do this?? I was fairly certain it can as long as the source footage is correctly interpreted.
Where you WILL run into trouble is with the problem that you have no control at all over how cheap players will handle this - especially over an HDMI connection that will more than likely stretch the 4:3 out to 16:9 and make everyone look like Danny DeVito.
Additionally, framing 4:3 in a 16:9 serquence will look strange on a 4:3 TV set - a little postage stamp in the middle of the TV.
