Two relatively simple things which I believe would significantly increase the usability of this template:
I see that this is an older post, and the answer may be found elsewhere. However, I too was encountering the same issue as described in line item 1. The solution for me was to to a create a multi-layer base map. The layers that were added to my base map were those I wanted to have displayed at all times, and not included in the summary panel. I used Pro to publish my layer as a Tile Layer. Then, in the web map, I moved the tile layer to the basemap. Instead of removing the feature layer from the contents, I simply turned it off which prevented it from showing up in the summary panel. See below link for more detailed information.
Choose basemap—ArcGIS Online Help | ArcGIS (scroll down to the middle of the page).
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