Your understanding is correct.
Once you create a DSA via mgmt UI, you will require to modify anything config related items via mgmt UI so it can be written to DXHOME/config/servers/dsaname.dxi file. If you modify the .dxi file manually after the fact, the mgmt UI will not reflect that change so it will be voided even though present in the .dxi file.
Once you create a DSA with command line tool (dxnewdsa) , you will not be able to see it in mgmt UI as that is a separate entity as DXagent component is not involved in this style of DSA creating process.
Hope this addresses your concern(s) and clears the doubt(s).