That setting is only configurable during the initial setup wizard. That said, simply synchronizing your user objects to Azure AD does NOT consume any licenses or incur any costs, so if that is your only reason for wanting to filter them out, you can just skip it.
Filter objects to synchronize by group
Is there any way to change this setting to enabled? Or do you have to completely re-install Azure AD Connect? Will that even work?
We want to change it so we only synchronise objects that belongs to a certain security group, as only a 10th of our users will use Office 365 and D365, and it will cost us a lot in Azure licenses if we synch all AD user accounts. I don't want to have to put them in a specific OU, as it will make administration harder.
Any help would be much appreciated.
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Yes, you can do a re-install to use that option.