To reproduce:
1. Open the attached project;
2. Open ShaderVariantTool: Window> ShaderVariantTool;
3. Make sure "level1" URP asset is set in Graphics Settings and "level2" URP asset is set in "SetPipelineAsset" game object;
-note: this asset (level1) has Additional Lights disabled, level2 asset (which is being set in runtime) has Additional Lights Per-Pixel.
4. Build the project and check shader variant count in the ShaderVariantTool or .csv file saved in your Project folder;
5. Clear Shader Cache;
6. Disable "SetPipelineAsset" in the scene;
7. Build the project and check shader variant count.

Expected result: URP asset that is being set on runtime should be taken into account while building (in this case shader variant count should be higher when SetPipelineAsset game object is enabled);
Actual result: URP assets that are not set in Graphics or Quality settings are not taken into account while building (the shader variant count remains the same), additional lights are not rendered when setting URP asset at runtime

Tested and reproduced on: 7.4, 8.2, 10.0.0-preview.26, master