Indian citizens are allowed to travel to Nepal by virtue of being an Indian citizen. What about those with Indian visas?
Having a visa for India does not allow you access to Nepal and conversely having a visa for Nepal does not allow you access to India. Nepal and India are two separate countries. The fact that they offer each others citizens visa free entry does not waive the rules for other nationalities.
To visit Nepal, you will need to meet Nepal's entry requirements for your nationality.