Matthia,
Did you try fresh the experience builder app after you configure the popup? Is the arcade expression customized in popup or already exist in feature attribute?
I cannot repro this problem. Is that possible that you share a data that can present the problem?
Some comments:
1. If you are configuring the popup from Map View, you have to save the map so that the configuration saved to the feature layer.
2. Refresh Experience Builder app to catch the configuration
3. The custom expression will be listed along with other attributes