Maybe you can get a hold of your problem by using the inheritance feature of checkmk folder? For every folder you create in WATO you can set properties which will be applied to all hosts inside it. For example at my former employer I used to create the following structure and apply settings to those folders:
Main Directory (/)
|_ Internal
|_ Customers
|_ Customer A (monitored at site customer_a)
|_ Network Devices
|_ Virtual Machines
|_ ...
|_ Customer B (monitored at site customer_b)
|_ Servers
|_ Remoteboards
|_ ....
|_ Customer C (bigger one, don't set the site (yet))
|_ Site 1 (monitored at customer_c_site_1)
|_ Servers
|_ Site 2 (...)
|_ Servers
|_ ...
Thus, you only have to set the directory when using automation which you could eg. name after some internal CustomerIds or other codenames which all teams understand altogether…
Another advantage of this is that when you create rulesets for eg. customer B and you apply the rules to the folder of customer B, you only need to restart the site of customer B and not all sites at the same time. There are checkmk users which needed even more separation. That’s when the CME was introduced.