Well.. deferred rendering (which shade-c uses) makes it practically impossible to use soft transparency due to the way lighting and scene composition are handled.
That's the main downside. At the same time, however, it allows for much faster lighting, an overall consistent look and things like shadowmapping, ssao, screenspace reflections, etc. can be implemented quite easily.

Now, in the case of shadec evo, there actually is a workaround implemendet to support one layer of transparency by using subsampling (only a small performance impact).

Long story short, if you want to use transparency, go with either 1-bit-alpha (alphatesting enabled) or limit yourself to said one layer of transparency.