I think you can do it by going to Optimize DVD and manually setting the video type for each clip... "NTSC" for 4:3 media, "NTSC Widescreen" for 16:9 media. (PAL would be similar, but I'm in the USA so I only know from NTSC. <grin>)

Let me give you an example. As an exercise, I ripped the music video and outtake clips from the "Star Wars" Episode I and II DVDs. When using DVD2AVI I noticed that the "Duel of the Fates" clip was 4:3, while "Across the Stars" and both outtake clips were all 16:9. I said to myself, "Self, how are you going to handle this?"

What I did was to create a new 4:3 DVDA project (I didn't want to hassle with making 16:9 menus; besides, I don't have a widescreen TV). I then imported all of the clips (after rendering them from AVI to MPEG2 with TMPGEnc), went into Optimize DVD, and changed the properties for all of the 16:9 clips from "NTSC" to "NTSC Widescreen." I then made the DVD, burned it with Nero, and tried it. Lo and behold, it worked perfectly.

So, unless I'm missing something, there's your answer: manually adjust the properties in Optimize DVD for each clip that doesn't match the project's aspect ratio.

(As an aside: the outtakes for both I and II are probably the best acting that Jake Lloyd and Hayden Christensen have ever done. <grin>)