We have the same problem but in AGOL.
We can create and use WMTS as basemaps in the AGOL Map viewer, but in any other js webapplication (ie agol templates viewers) the wmts basemap doesn't 'appear.
Searching with Firefox firebug we noticed this error while we try to switch from standard basemap (tiled rest map service) to WMTS basemap from the basemap gallery:
TypeError: this.tileInfo.spatialReference.toJson is not a function
we use the same spatial refeence ( webmaercator) and the same tiling schema.
Any help is appreciated.