How the RGB image is created from separated bands (not metadata file) in SNAP? In other words, how three separated bands is integrated into one file?
The RGB view is just a visual thing, the original product is not altered, nor is a new product written on your drive. If you want to store the color information permanently in one raster you can select
File > Export > Other > View As Image > GeoTiff with geoinformation
I mean in SNAP, is there a tool such as "layer stacking" in ENVI?
Raster > Geometric Operations > Collocation
Radar > Coregistration > Stack Tools > Create Stack (also works for optical data)
Radar > Coregistration > Coregistration (works best for radar data)