If your alternate versions are limited to what layers are turned ON by default you can use the Share Widget in WAB and selecting the link option "Remember layer visibility." This can generate a unique link that can re-create the current visible layers and zoom location. We have used this technique to have a single app that starts with a zoning background in one version and an aerial in another. Looking at the Esri doc note that there are potential issues if lots of layers are involved, as there are certain limitations on URL length.
If your alternate versions involve different tools or other configurations across multiple apps we'll have to see if anyone else has any tips.