On the function that sets the logic for ion-alert to present, pause the video, then show the alert. To show an element as an overlay on the video, there is a hack to achieve this. I am going to assume it will work with ion-alert the same way.
You could set z-index of ion-alert as mentioned here. Set its z-index to 2147483647. Please check it, I dont have time to do so. Also, I cannot speak about compatibility of this fix with all browsers.
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