[Bug] visualMap component doesn't render all scatter points when rendered progressively

### Version

5.6.0

### Link to Minimal Reproduction

https://codepen.io/ddegan/pen/myegeja?editors=0100

### Steps to Reproduce

1. Open the provided link, hover on points, everything is ok
2. Click the "Change visual map dimension" button. (this will setOptions changing the visualMap component, adding a size visual map)
3. Hover one bubble and see that some values disappear (but if you hover the points are shown)

### Current Behavior

Lots of points are removed from the chart, while they are shown when hovered.

### Expected Behavior

All points should be present after changing the visual map options

### Environment

```markdown
- OS: Window 11 pro
- Browser: Chrome 140.0.7339.81
- Framework: no framework
```

### Any additional comments?

Don't know if it's related to https://github.com/apache/echarts/issues/20845 but the behaviour is similar.
Missing points are not visually obvious unless you hover them.
End users may never notice that some points are absent, which can lead to wrong conclusions or misinterpretation of the data.
This impacts the reliability of scatter/bubble charts, especially in use cases like analytics dashboards or scientific data visualization, where every single point matters.

Disabling progressive rendering is not an option for me since I'm dealing with big datasets that must be rendered progressively to smooth the UX.