The "Merge" tool in ArcMap is practical and fast, but in ArcGIS Pro, you have to select field by field so that when the information from both layers is integrated, it is displayed correctly in the result and needless to say when "Model Builder" passes it , practically one must generate a temporary and then copy so that the configuration of the fields respects it, also here is a detail when you want to work Geodatabase, it does not let you send an error, instead if you send it "shapefiles" it just works.
Hi, if the problem in the Merge tool is that only the fields of the first input dataset are visible in the Field Map, please try the workaround using the Add Many button described here: