C'mon you know answers to these questions, so why ask them?
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But the better question is, why are we still encoding with VFW/AVI programs?
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I didn't know there are hardware players which play MP4+AC3 or MKV+AC3. I didn't know you can mux AC3 in MP4.
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Why doesn't virtualdub(mod) output directly to .mp4 or mkv?
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Because the dev. didn't program that (I'm not sure whether they have plans for this). Saidly, the dev. of VDubMod seems being stopped.
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Where are the encoding tools that will output native MVK and MP4 files?
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These will come some day.
About bond's problem. Let me ask the following question to put it into perspective: Suppose we do 2-CD rips (because we want to have the AC3 stream), why do we need b-frames at all?