Regarding the error, yes it would happen if not using the new Web.config because the control references for the comment widget and some other things were added and without them errors will happen.
Yes, on the initial release I forgot to make the default web.config be the medium trust one so Web.config in the package was full trust and web.mediumtrust.config also existed. I realized that mistake several days ago and corrected the package for MS SQL .NET 4 becuase it is required to be configured for medium trust before I can submit the update to the web app gallery.
I need to double check but I'm 99% sure that web config setting for medium trust has not been used in a long time because we found another way to detect trust level. I will look into that and remove that setting if I'm correct. The only difference these days between the full and medium trust config files is the NeatUpload settings.