You are talking about separate video files on the DVD, right? It is possible to put mixed aspect ratio clips on a single DVD and have them work correctly, but they have to be on the disc as separate files. Maybe you can pre-render to MPEG-2 so the right flag (4:3/16:9) is inserted and DVD-A doesn’t re-render them?
If the clips need to be mixed into the same video file, you have 2×2 choices, of course:
(1) Project at 4:3 and
(a) letterbox the 16:9 sections (black bars top/bottom)
-or-
(b) zoom in on the 16:9 clips, cropping the left/right
(2) Project at 16:9
(a) pillarbox the 4:3 clips (black bars left/right)
-or-
(b) zoom in on the 4:3 clips, cropping the top bottom
I guess it depends on which aspect is dominant (e.g., you’ve got 90% 16:9 footage with a little 4:3), but if it were close to 50/50, I think I’d go with the more modern 16:9 aspect project and (2b), zoom and crop the 4:3 clips. The big danger here is that the 4:3 clips will suffer a quality hit zooming in on them.