The Ignika could and did, that is true. It was only able to do that because the masks in question were already alive.
The first time, the Red Star didn't change the Inika's kanohi. They had already had their matoran masks confiscated by Karzhani and replaced with (powerless versions of) their inika masks when they passed through his realm.
If we're just going to use the standard toa stone method of transformation, our characters will have to start with the (disk-based) type of masks they'll have as toa. Either that or after they get transformed, the suva opens up like it did for the Toa Metru when they chose their tools, only the Kongero Nui suva will also contain a selection of great kanohi.