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there is no out-of-the-box support for you to manage brownfield, customers must have solutions tailored for the use cases.
the 2 problems in your use case requires contradicting solutions: 1 indicates you don't want the service to own the device conf...
the 2 problems can be solved by the new brownfield service protection in 6.5:
starting with a service configuring 1 if:
% show devices device ex0 config sys interfaces interface eth1 | display service-meta-data/* Refcount: 1 */description service;/* ...
a general comment on service design: the service callback should be idempotent(https://nso-docs.cisco.com/guides/development/core-concepts/implementing-services#ch_services.fastmap), the complex computing function in your service callback makes me wo...
I can't reproduce your observation that "the package operates also on devices with NED ids not included in package-meta-data.xml supported-ned-id tags", if I have:
1 2 versions of the same ned loaded, let's say 1.0 and 1.1
2 a template with no <?if-...
now I'm not sure what the question really is... do you want to be able to load the service package? or do you want to know why having <supported-ned-id> in package-meta-data.xml gave you "no effect"?