As mvt driver of OGR using TILING_SCHEME=crs,tile_origin_upper_left_x,tile_origin_upper_left_y, tile_dimension_zoom_0 to support custom tiling scheme, I think mbtiles should not to be limited to web mercator.
I assume mbtiles will be a generic spatial data format in the near future. a generic spatial data format should not to be constrained to only one tiling scheme.