optimize_layout reports "Resolved" but overlaps persist after apply_changes=true

## Bug Report

**Tool**: `optimize_layout`

## Steps to Reproduce

1. Insert two overlapping vertices (e.g., both near canvas (500, 100))
2. Call `optimize_layout(strategy="resolve-overlaps", apply_changes=true)`

## Expected Behavior

- `finalOverlaps: 0`
- `find_overlapping_cells` confirms no overlaps remain

## Actual Behavior

- `finalOverlaps: 1` in diagnostics
- `recommendations` says "Resolved" (false positive)
- `find_overlapping_cells` confirms overlap still exists after the call

## Impact

`optimize_layout` cannot be relied upon for layout correction. The false-positive success message makes the bug hard to detect. Workaround: calculate non-overlapping coordinates manually before inserting cells.