The key difference is #eKuber originating #DBT is a real #DBT at originating end (while still not so direct at recipient end), where as #Aadhaar based #APB is having a central intermediary on top of agency bank and hence has cost of 2 intermediaries & cannot be called true #DBT
HR Khan on #eKuber in 2013 - Challenges and Concerns of the Central Bank: Opportunities and Role for the Commercial Banks - Harun R Khan https://www.rbi.org.in/SCRIPTs/BS_ViewBulletin.aspx?Id=14283
Reserve Bank of India - RBI Bulletin

e - Kuber Guidelines.pdf

It is still sound alternative and given that #NEFT is free of charge, it probably saves exchequer some money if #G2P payments are routed directly from treasury accounts in #eKuber to beneficiary accounts via #NEFT instead of #APB and incurring cost.
e-Kuber portal

Integration of salary payment

State's treasury account held at RBI's CBS #eKuber is connected to #NEFT and the payment goes through. Since its #NEFt, there is no upper limit to the transfer. All that is needed is beneficiary's account number and funds in treasury.

What is #eKuber ?

e-Kuber is the Core Banking Solution of Reserve Bank of India. e-Kuber Is being widely used by central and state governments for their financial management.

But how does the payment go through ?

Though Rythu Bandhu (RBS) needs #Aadhaar, the payment takes place without the #APB infrastructure for #DBT, instead tried cheque based disbursal before moving to #DBT from RBI #eKuber