It applies down to individual values.  The following exerpt may provide
answers to your questions:

[Quote]

Atomicity and Hive Recovery in the Registry

The Registry ensures atomicity of individual actions. This means that
any change made to a value (to set, delete, or save) either works or
does not work: The result will not be a corrupted combination of the old
and new configuration even if the system stops unexpectedly because of
power failure, hardware failure, or software problems. For example, if
an application sets a value for an entry and the system shuts down while
this change is being made, when the system restarts, the entry will have
either the old value or the new value, but not a meaningless combination
of both values. In addition, the size and time data for the key
containing the affected entry will be accurate whether the value was
changed or not changed.

Flushing Data

In Windows NT, data is written to the Registry only when a flush occurs,
which happens after changed data ages past a few seconds, or when an
application intentionally flushes the data to the hard disk.

The system performs the following flush process for all hives (except
for the System hive):

1. All changed data is written to the hive's .log file along with a map
of where it is in the hive, and then a flush is performed on the .log
file. All changed data has now been written in the .log file.

2. The first sector of the hive file is marked to indicate that the file
is in transition.

3. The changed data is written to the hive file.

4. The hive file is marked as completed.

Note If the system shuts down between steps 2 and 4, when the hive is
next loaded at startup (unless it's a profile hive that is loaded at
logon), the system sees the mark left in step 2, and proceeds to recover
the hive using the changes contained in the .log file. That is, the .log
files are not used if the hive is not in transition. If the hive is in
transition, it cannot be loaded without the .log file.

A different flush process is used for the System hive because it is an
important element during system startup and is used too early during
startup to be recovered as described in the previous flush process.

The System.alt file contains a copy of the data contained in the System
file. During the flush process, changes are marked, written, and then
marked as done. Then the same flush process is followed for the
System.alt file. If there is a power failure, hardware failure, or
software problems at any point during the process, either the System or
System.alt file contains the correct information.

The System.alt file is similar to a .log file except that at load time,
rather than having to reapply the logged changes, the system just
switches to System.alt. The System.alt file is not needed unless the
System hive is in transition.

[end quote]

http://www.microsoft.com/resources/documentation/windowsnt/4/workstation/reskit/
en-us/23_regov.mspx

John.