What versions of SNAP and QGIS are you using and what projection/CRS is used in the GeoTIFF files? It could be useful to post the output of gdalinfo for a Landsat 8 GeoTIFF.
The unique advantage of SNAP is the detailed sensor-specific support A survival guide to Landsat preprocessing gives an overview of Landsat workflows with emphasis on ecology. Landsat How to Use Data mentions ArcGIS, Processing Landsat 8 Using Open Source Tools (mapbox), and MultiSpec.
ALOS 2 Level 1.5 data problem is another example of SNAP’s limitations for unsupported sensors.