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Sorry for digging this out. I just wanted to say that I've finally found a solution, though not with AviSynth. Maybe it can help someone else.
The program is called AviUtl and is a japanese VirtualDub-like program. And with its DirectShow plugin it's the only encoding program I've found so far which does exactly what it says: Loading the file with DirectShow, exactly like media players (inclusive linked segments)
The drawbacks: It's only in japanese and chinese; it's like VirtualDub, so only VFW and .avi; it seems to mess up the audio sometimes (I didn't look into it yet, though)
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