Currently, a field like this:

      - input:
          range: SourceInput
          slot_uri: schema:object
          description: >-
            The inputs to this source.
            If the source represents external import of a sequence, it's empty.
          required: false
          multivalued: true
          inlined_as_list: true

Will get transformed into a pydantic model like below, where the default value is None.

input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
        default=None,
        description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
        json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
    )

Instead, you may want the default value to be an empty array (e.g. if this represents a relationship field), so instead of default=None, in pydantic you would want something like default_factory=list.

Is there a supported way for this already? (I don't think it's possible using ifabsent).

This seems like a fairly common use-case. If there is a ready solution, I am happy to contribute the information to the documentation.