Custom Variables are the custom dimensions of the previous version of Google Analytics. A large part of applications are still using older software, which is using custom variables and not custom dimensions. In Google Analytics, Custom Dimensions are referenced by their name as shown below in the image. This is not the case with custom variables.
The custom variables are referenced by their number. In this case, the App version data on newer apps can be found by using the App version reference in a custom report. If you are using an older application, the app version data is saved in Custom Variable (Value 2).
By using this reference, you will be able to see the App version data for versions before Google Tag Manager was implemented.
If you have questions regarding your data or the differences between Custom Variable and Custom Dimensions, feel free to contact us.