Eliminate Native AOT warnings from MSBuild-backed CLI commands

### Describe the bug

Enabling the MSBuild-backed command handlers in the Native AOT `dotnet` CLI currently produces trim/AOT diagnostics from the command layer's transitive dependency closure. The infrastructure-only layer publishes with zero detailed diagnostics; the warnings appear only once resolver activation and project-backed commands are enabled in #55497.

With `TrimmerSingleWarn=false`, the current warning set is 5 IL2026 diagnostics and 13 IL3050 diagnostics. The concrete origins are Newtonsoft.Json LINQ-to-JSON dynamic/public API paths and runtime `System.Linq.Expressions` / `Microsoft.CSharp` dynamic-binder paths.

### Steps to reproduce

1. Check out the command-enablement branch from #55497 after its infrastructure dependency from #55441.
2. Publish `src/Cli/dotnet-aot/dotnet-aot.csproj` for Native AOT with `TrimmerSingleWarn=false`.
3. Inspect the emitted IL2026 and IL3050 diagnostics.

### Expected behavior

The MSBuild-backed Native AOT command layer publishes without first-party or dependency trim/AOT diagnostics, and the temporary IL2104/IL3053 `WarningsNotAsErrors` policy can be removed.

### Actual behavior

The detailed publish reports 18 diagnostics (5 IL2026 and 13 IL3050). #55497 must temporarily keep IL2104 and IL3053 as non-errors so its Native AOT publish can complete while the dependency closure is migrated or annotated.

### Is this a regression?

No. This warning closure becomes reachable when #55497 enables the MSBuild-backed commands in the Native AOT CLI.

### Are there any workarounds?

Keep only the IL2104 and IL3053 aggregate diagnostics in `WarningsNotAsErrors` in the command-enablement layer. Do not apply that policy to the infrastructure-only #55441 layer, which publishes with zero detailed warnings.

### dotnet --info output

N/A

### IDE version

N/A

### Other details

Track the exact detailed warnings with `TrimmerSingleWarn=false`; do not infer reachability merely because an assembly is referenced. The NuGet packages.lock.json read-path migration materially reduces the Newtonsoft closure, but remaining writer/public API metadata and dynamic-binder roots still need separate attribution before removing the temporary policy.