I am migrating to Map Components and it is a steep up hill.
I have a Popup Template configured on my layer and my Popups are visible. I also have a custom div which is appended into map component. The position of that custom div is "absolute", or can be "relative". The Popups are visible under the custom div not over. Any way to overcome.
This is a current limitation of the Popup widget in map-components. We do have a beta Popup component you can try in some cases (does not work with Search component yet).
https://developers.arcgis.com/javascript/latest/release-notes/#popup-component-beta
I did a video recently on the Popup component