^ A couple of months ago, I decoded a MLP file with ffmpeg, and indeed, the resulting WAV file also had some "additional silence" at the end. I haven't studied the source-code of the DVD-Audio plugin for foobar2000, so I can only hope/assume its author has done the job well.
But back to the Master Audio example --- the fact is, if you use the DTS StreamPlayer for decoding, you always get a bit-exact output. BTW, one of the reasons for the "non-existence" of an open-source Master Audio decoder is, it would require a bit-exact decompressor for the lossy "core", in the first place.