[Bugfix] restore legacy stage config precedence

[xiaohajiayou]

PLEASE FILL IN THE PR DESCRIPTION HERE ENSURING ALL CHECKLIST ITEMS (AT THE BOTTOM) HAVE BEEN CONSIDERED.

Purpose

This PR fixes an unintended behavior introduced by #2076 in the legacy
load_and_resolve_stage_configs path.

After #2076, CLI runtime args can override default stage configs. However,
CLI default values also started participating in the merge and could override
the YAML's default stage config values even when the user did not explicitly
set those CLI args.

This PR restores the previous behavior for the legacy loader by switching
prefer_stage_engine_args back to True when loading model-default stage
configs.

Behavior

Before this fix:

• CLI defaults could override default stage YAML values
• default stage configs could be unintentionally polluted by CLI defaults

After this fix:

• stage YAML defaults take precedence again in the legacy model-default load path
• only intentional runtime overrides should affect resolved configs

Rationale

The affected path is the legacy load_and_resolve_stage_configs chain, which
is planned to be removed by the config refactor tracked in #2072.

this pr is a minimal rollback of the legacy precedence behavior, intended as a temporary fix until the #2072 refactor is completed.

---

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