I’m wondering whether these machines are under the same of different vCenter server?
Either way there wouldn’t any issues related to monitoring custom virtual infrastructures through one Veeam installation, providing you’ve specified sufficient resources for this machine.
Though, the approaches may vary.
In case of different vCenters, just add them to VeeamOne server, making sure that specified vCenter account does have required permissions (that are pretty good covered in Veeam One Deployment Guide).
In case of one vCenter, it might be worth grouping VMs in desired way using Business View functionality. For instance, VMs of customer#1 -> Group#1, etc. Such scenario will guarantee cheer convenience, as well as, efficiency.
As to security problems, you might want to elaborate on it little bit, so that, we can understand what particularly you’re concerned about.