Yes! Customers are able to select which hosts they want to run APM+Pro vs Pro-only on.
There is a switch to flip on each local datadog-agent in order to have it report APM data, see more here: https://docs.datadoghq.com/tracing/setup/. Thus customers remain in control of which hosts are counting towards their APM+Pro total.
Note that Enterprise customers must run all their hosts on Enterprise (ie, they cannot run some on Enterprise and others with Pro).
More information about bill calculation is available in this article: https://help.datadoghq.com/hc/en-us/articles/216099263-How-are-my-bills-calculated-each-month-.