I have applied a definition query to a feature class and chose to export features to my project database. The result is an exact copy of the original feature class, including features that did not meet my definition query. I know that if I chose to export features with a selection Pro would only export the selected features. This should be the case with a definition query as well.
I understand that this is using the copy features tool. However, in Desktop both the export option and the copy features tool will only copy the features that meet the definition query. Creating new feature classes from layers with a definition query is a regular part of our workflow and not having this ability increases the time it takes to perform regular tasks.