For the purpose of immigration all of Schengen can be considered on "country", and flights between countries in within the Schengen area operate pretty much the way domestic flights do elsewhere. Within the Schengen area such flights are called "internal" flights.
Airport in the Schengen zone have usually two areas, an "International Area" and a "Schengen Area". Flights to other destinations within the Schengen zone leave from this Schengen area. Immigration is done between the Schengen and the International areas, and this in both directions (arriving and leaving).
So coming from India and arriving in MUC or CDG you will need to get from the International Zone to the Schengen zone. To do this you will need to pass immigration, where they will check your Visa, and stamp your passport. Arriving with a type D visa from a different country is not an issue. People do that all the time.
You then board your flight to GVA, and then when you arrive there can just go through customs and walk out of the airport after picking up your luggage...
Two further notes:
- MUC is a much more agreeable place to change planes than CDG. The airport is very efficient, and build to make short transfers feasible. That is why LH offers you this.
- Currently the COVID situation may mean that you cannot at the moment travel to Europe at all. Do check that.