Unfortunately the number of inputs (and outputs) is hard-coded in a VST. The DAW needs to know in advance how many inputs there are, so when the plugin is initially scanned it reports back the number of inputs and SONAR files that information away in the registry. It can't be changed on the fly.
FabFilter in the past has offered multiple versions of plugins for that reason. Pro-C, for example comes in four flavors: mono, stereo, mono with sidechain and stereo with sidechain. Timeless2 has two versions, with and without sidechain. But they've said they're getting away from that model and future products will only have one version. Pro-MB, which is very close to MDynamicEQ in functionality, comes in just one configuration: stereo + side chain (4 inputs).
What all that means is you're going to have ongoing problems with Mixbus until they figure out how to support plugins with more than two inputs.
Or if you can convince Vojtech to make a non-sidechain version. It wouldn't hurt to contact him and ask: info (at) meldaproduction.com.