As soon as you start using Flexi for the first time, the regular layout popup is assigned. Which has default in nature and do not have any customization on settings or anywhere. You have to hard code to edit it.
Flexi introduced custom popup layout which can be changed from the Flexi settings under Detail tab.
By changing into shortcode by changed popup="custom" into flexi-gallery shortcode.
After this you have to make settings at custom - popup layout. Here you can show hide different elements at desired location. Each location is denoted by the numbers