Hello eros,
I am trying to answer your queries in points, if I miss anything, please feel free to ask.
1> Is seems some widgets are there but not visible in the customize area. Possible?
Response : When you change the number of footer widgets in customizer, please refresh the page after saving to view the effects. You can also check widgets in Appearance > Widgets.
2> Relation between SuperMag theme and SuperMagPro theme
Response : As you see there are many widgets areas, many widgets and more customizer options in SuperMagPro than SuperMag, the only option that will migrate will be common customizer options from SuperMag to SuperMagPro and you can always change any option in SuperMagPro theme.
Using SuperMag theme 1st and then SuperMagPro theme won’t harm anything to SuperMagPro theme. Instead we think using SuperMag theme first make you more familiar to SuperMagPro theme.
Again thank you for choosing SuperMagPro theme, if you have further query please fell free to ask.
Best Regards,
AcmeThemes