Some things which come to my mind in this regards:

Use of a removed function or use of a removed extension are in principle two distinct issues, so yes, in practice that could mean that you'd get two messages, but one change in the code will remove them both.
Keep in mind that sniffs can selectively be turned off.
The ability to whitelist specific functions targetted by the deprecated extensions sniff as implemented in Add ability to whitelist functions from a custom ruleset to the removedExtensions sniff. #130 could also be extended to a new extensions sniff.
Currently most sniffs do not have modular error codes. This means if you want to disable a particular error message - for example the message about json_encode() - you would have to disable the complete NewFunctions sniff. More modular error codes would go a long way to keeping this library useful while still allowing for having some select compatibility functions.

Ruleset code example:

<!-- Current -->
    <rule ref="PHPCompatibility">
        <exclude name="PHPCompatibility.PHP.NewFuntions" />
    </rule>

<!-- With modular error codes -->
    <rule ref="PHPCompatibility">
        <exclude name="PHPCompatibility.PHP.NewFuntions.json_encodeFound" />
    </rule>

What do you think ?

Uh oh!

New Extensions sniff ? #150

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