In Convert, click on Options, check Apply DSP and select DSP Options. In Output Format, set 352, 704, and > 768 to the final format you want - like 176.4 KHz. I am away from home and only have MC 20 on this computer, but I think the 704 and 768 options are in MC 21. I have 384 KHz as my maximum.
When you convert DSD to flac you need to filter out high frequency noise. By default, MC uses a low pass filter at 24 KHz and 48dB/octave. I think that is too aggressive and think something like 50 KHz at 48dB/octave is more appropriate. I believe the 50 KHz filter is the SACD standard. The default filter is set in Tools- Options - Audio - Advanced - Input Plugins - DSD. I disable the filter there and add the 50 KHz at 48dB/octave filter in the DSP options in Convert - in Parametric Equalizer.