Hi Candice,
First, let's get on the same page for terminology. When you say "I am creating several maps in different layouts and different map frames using the same features in ArcGIS Pro". I'm assuming that you have several map frames in different layouts that point to the same map. This is what the Stack Exchange thread refers to and is not supported by ArcGIS Pro. Though map frames do control some "map properties" such as extent - it does not control many map properties such as layer visibility, or any layer properties. These are are controlled by the map. Think of the map frame much like a map view - it is a view of the map. You can layer properties while working with a map view or a map frame, but all other views linked to this map will see these changes as well.
From the help topic - Add and modify map frames—ArcGIS Pro | Documentation
Note:
While the map extent of each map frame is independent of other map frames, the contents of a map frame's map are not. A map frame is just like having another map view open. For example, if you select some features on a map, those features are selected in all open views of that map—including in map frames. Likewise, if you turn off a layer in one view, it turns off in all views. Layer properties cannot be set per view.
Until we engineer a way to either version maps or "freeze" map frames with a given state of a map (similar to ArcView) you will need to manage your map states by either toggling the layer visibility as needed or by created a new map for each map state that you want in different layouts.
Here is a thread on Ideas site that has more info:
https://community.esri.com/ideas/18312
Hope this helps,
Tom
