Multistore feature in PrestaShop is great feature to build many shops that can be controlled from one back office. This means that with this feature, you can manage many customized shops, which share many common elements. For more efficiency, you can even create groups of shops etc. Each of this shop can have own unique configuration and unique modules that are enabled. Pretty clean urls module fully supports multistore configuration, but in this case - it requires to configure it carefully.
Okay, for example let's say that you've got several stores: store A, store B, store C, store D. For some of the stores you want to enable the module, for some of them not. In this case, before you will configure the module you have to select store from "shop context" menu:
Then go to the modules > modules section and install, enable and configure the module for selected shop context. Do the same for each shop available in the multistore feature for which you want to activate the module and remove id from urls. If you dont want to remove id from urls in selected shops - select this shop from multistore shop selection and disable the module for selected shop.
Simply saying:
Shop | Want friendly urls without ID |
Selected shop In multistore selection |
What to do |
Store A | yes | Store A | Enable and configure the module |
Store B | yes | Store B | Enable and configure the module |
Store C | no | Store C | disable the module |
Store D | no | Store D | disable the module |
Do the same for configuration of schema of urls. For shops with enabled module - remove the {id} from schema of urls section, for shops with disabled module - use default values (details on documentation page that i linked)