3D WebView's default 3D rendering mode works by rendering web content to a texture that is shown in Unity. This approach works efficiently on most platforms, but on iOS, the platform's native APIs for capturing pixels from the browser is relatively CPU intensive, which can sometimes cause a phone to heat up. I'm tracking this issue and will update this article if I discover a way to completely prevent it in the future. In the meantime, here are options to prevent it:
Use Native 2D Mode if possible. Native 2D Mode drastically improves performance and does not lead to heating.
If you're unable to use Native 2D Mode for your use case, then another option is to use iOSWebView.SetTargetFrameRate() to reduce the target frame rate. You can also reduce the WebViewPrefab's Resolution, which reduces CPU usage.