You can use any encoder to encode KVCDs, but the best quality is given with TMPGEnc, and the KVCD process is optimized with TMPGEnc in mind. If you still want to try, does MainConcept have a CQ mode (1-pass VBR)? And does it allow you to change the GOP and Quantize matrices.
If it does, just install the free version of TMPGEnc, download the KVCDx3 templates, Load them into TMPGEnc click Settings and copy the parameters to MainConcept. Only encode the video with MainConcept though, use HeadAC3he to do the audio, then mux them together afterwards with BBMPEG.
The quality won't be as good as if you use TMPGEnc though...