NIC provides a Direct-API for registering eInvoices. "Direct-API" means that the API endpoints on the NIC servers can be accessed directly by the tax-payer (i.e., without having to route the data via any intermediary or GSP).
GSTN has recognized that eInvoice data is confidential & embodies trade secrets. Pricing information in particular is something that companies protect zealously. Large companies often spend an enormous amount of money on implementing on-premise ERP solutions precisely for this reason. Invoice data is too precious to be stored on a cloud-based ERP.
It is one thing for one data-point (pricing of a particular item at a particular time) to be compromised. It is much worse when detailed invoicing data ends up being gathered over a period of time into a database. Significant analysis can be performed and inferences drawn from such databases. ("Big Data", "Data Harvesting"). Needless to say, this data is of immense competitive value.
Many CIOs, CFOs and Information Security professionals understand this, and are reluctant to route data via third-parties. There are other benefits to going direct as well. It reduces the number of hops, and therefore reduces the latency and minimizes the points of failure. Further, you are at no risk of being charged annual or per-transaction fees by anyone.
Given these significant concerns, it is logical for NIC to provide an API which tax-payers can consume themselves, and route the data to NIC directly. Hundreds of Companies (500Cr+ turnover) have adopted the direct route to implement their eInvoicing. GSTN has also included eWayBills in this API, which means Taxpayers can now generate eWayBills along with eInvoicing as well.