As far as I know, that is not possible. Maybe something has changed recently, but when TrueHD is extracted from an M2TS you will get 2 streams, the AC3 and the TrueHD (unlike DTSMA-HD which will have the core and meta data as one file). The AC3 stream is only for backward compatibility and if you need that in your mkv then just include the second audio stream.
QB
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