I've been working on a application that will read data from a number of site collections in SharePoint 2016. At present I've been adding the user to each site collection as a site collection administrator but noticed that I can add the user on the web application under 'Manage Web Applications' selecting the web application and clicking on 'User Policy' and adding the user with 'Full Control'. There is a warning about adding a policy, should this be avoided? Or is it ok to do this if the user/policy is not repeatedly added/removed?
Adding or updating Web application policy with new users or groups will trigger a SharePoint Search crawl over all content covered by that policy. This can reduce search crawl freshness and increase crawl load. Consider using security groups at the policy level and add/remove users from security groups to avoid this.