Having read some reviews online, I can say that there is not much difference in the colleges but the approaches to studies or academics, placements, etc. vary to a great extent.
Now, when coming to the certification level, your degree certificate will have the name of your autonomous college that comes under VTU as it will be issued by VTU. But the college will not be mentioned if your degree is from VTU.
You need to be aware of the differences between the two in the aspects like faculty, facilities, and placements. In the end, these 3 are the most important things that depict the status of an institute.