docs: update automatic migration compatibility notes

[clockwork-labs-bot]

Summary

• Update automatic migration docs to reflect empty-table removal behavior.
• Document accessor/source-name metadata changes and index accessor rename limits.

Audit notes

• Baseline: latest merged bot/docs-audit PR docs: fix daily docs audit findings #5516 (merge commit a2d2fed).
• Commit-impact pass checked recent master changes touching schema auto-migration, C# runtime/AuthCtx internals, and NativeAOT-LLVM notes.
• Skills checked against public docs: CLI, concepts, C#/Rust/TypeScript/C++ server, C#/TypeScript/Unity/Unreal clients, MCP.

Validation

• pnpm build