When the compatibility tag is explicitly disabled in 6.0 configuration xml, it is enabled in the converted one.

The following xml:

...
    <namedCache name="withCompatibilityDisabled">
        <compatibility enabled="false"/>
    </namedCache>
...

is converted to:

        <local-cache name="withCompatibilityDisabled" statistics="false">
            <compatibility/>
        </local-cache>

And, the config.compatibility().enabled() returns true.

UPDATE:
This also refers to storeAsBinary tag.
The async element of the singleFile or store tag is also enabled in the converted XML, even if it is disabled in 6.0 config xml.