[PHPUnit] ignore E_USER_DEPRECATED notices

| Q             | A
| ------------- | ---
| Bug fix?      | yes
| New feature?  | no
| BC breaks?    | no
| Deprecations? | no
| Tests pass?   | yes
| Fixed tickets | 
| License       | MIT
| Doc PR        | 

This updates the PHPUnit configuration files that have not been
updated in #12705.