You do not have to send your physical passport.
The e-visa for Nepal requires 2 steps. First you need to fill in a tourist visa application form. Once it is approved, it will be sent to your email. You will need to print that document to present it when you enter the country. With this document (payment registration receipt), and your passport, you will complete the processing of your visa upon arrival in Nepal. Your passport must be valid for more than 6 months starting from the date of entry.
If you need to apply for another type of visa other than the tourist visa, and you have to apply through a physical embassy. We advise you to always send your documents sustained with damage or loss insurance.