Contrary to popular belief in India, Nepal was never legally a part of the Modern Day India. It has maintained its independence for centuries before the Mughal Empire or the Delhi Sultanate as well. The concept of Statehood is rather new to the Indian subcontinent. While historically and culturally the two Nations have tremendous similarities, but in terms of country, they are a completely different entity altogether.
The Nepalese and Indians have different national rhetoric and political system. While the Indian State was formed as a result of British Colonization which is a reorganization of various Indian states that came under the British suzerainty in the late 18th and early 19th century, Nepal on the other hand, while similar to many other Independent Indian states, was never officially conquered or colonized by the British. It managed to maintain its autonomy from the British crown and also established foreign relations with other countries during the same time.
It had its own currency, foreign emissaries, army and Laws and hence could be easily deifferentiated from other Princely states of the subcontinent. Nepali soldiers were also instrumental in suppressing the 1857 Indian Uprising. Even during the Indian Independence movement the major political parties of India didn’t have any influence on the Nepalese people. This all shows glaring difference between the two countries.