Standard keyboard layouts expect that you have always caption, shiftedCaption and if you have symView defined it expects symView2 also. You can bypass these restrictions by copying CharacterKey.qml and creating own version of it which implements exactly what you need for Hebrew keyboard.

Popper may also cause unwanted issues with custom keyboards not having all layers of characters and symbols in it.

Be warned that messing with layouts.conf may break software updates (SSU). Jolla should creates a method how to select which keyboards are available in selection list and officially support third party keyboard layouts. Until then you should create you own keyboard specific .conf file to layouts directory and live with all those languages in the list. You can however define same keyboards even multiple times and thus list you favorite ones easily accessible in the beginning on keyboard list before the system list.