This is a very old post but we have just experienced this error "All the machines in the site are required to have same license" at 10.7.1, using Microsoft Azure machines. For anyone experiencing this error, my advice is to check the time/date/region settings on the two machines.
We used the same Keycodes file across 2 machines in the site. We noticed that at the REST endpoint, the expiration date of the licence was reported slightly differently between the two machines, hence the error message. In our case the difference appears to have been caused by one of the two machines being changed from a US region to a UK region and back again (before the installation of ArcGIS). Somehow the system clock was left permanently slightly out. In our case the solution was to blow away the machine whose region had been changed and provision a new one.