We already support setting configuration values, either:
 (1) set any internal section, i.e. groups starting with [.intern*].
     Those values don't ever interfere with that the user can
     configure.
 (2) set individual properties that overwrite user configuration.
     When doing that, we record the value from user configuration
     and on load, we reject our internal overwrite if the user
     configuration changed in the meantime.
     This is done by storing the values with ".set." and ".was." prefixes.

Now add support for "atomic sections". In this case, certain groups
can be marked as "atomic". When writing to such sections, we overwrite
the entire user-provided setting.
We also record the values from user configuration, and reject our
internal value if we notice modifications. This basically extends
(2) from individual properties to the entire section.