Você precisa estar usando o Apache v2.4.10 ou superior e como o Ubuntu 14.04 LTS vem com v2.4.7, é mais provável que você esteja usando. A documentação menciona isso brevemente no início dos documentos de diretiva de cabeçalho:
Compatibility: SetIfEmpty available in 2.4.7 and later, expr=value available in 2.4.10 and later
Eu corri alguns servidores para confirmar que isso funciona
Apache v2.4.12:
root@ubuntu-server:~# lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 15.10
Release: 15.10
Codename: wily
root@ubuntu-server:~# cat /etc/apache2/sites-enabled/000-default.conf
<VirtualHost *:80>
Header set foo-checksum "expr=%{md5:foo}"
</VirtualHost>
root@ubuntu-server:~# apachectl -v
Server version: Apache/2.4.12 (Ubuntu)
Server built: Jul 24 2015 15:59:00
root@ubuntu-server:~# service apache2 reload
root@ubuntu-server:~# curl -I localhost
HTTP/1.1 200 OK
Date: Mon, 07 Mar 2016 21:15:38 GMT
Server: Apache/2.4.12 (Ubuntu)
Last-Modified: Mon, 07 Mar 2016 20:57:04 GMT
ETag: "2c39-52d7bb502f118"
Accept-Ranges: bytes
Content-Length: 11321
Vary: Accept-Encoding
foo-checksum: acbd18db4cc2f85cedef654fccc4a4d8
Content-Type: text/html
mas não no Apache v2.4.7:
root@ubuntu-server:~# lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 14.04.4 LTS
Release: 14.04
Codename: trusty
root@ubuntu-server:~# cat /etc/apache2/sites-enabled/000-default.conf
<VirtualHost *:80>
Header set foo-checksum "expr=%{md5:foo}"
</VirtualHost>
root@ubuntu-server:~# apachectl -v
Server version: Apache/2.4.7 (Ubuntu)
Server built: Jan 14 2016 17:45:23
root@ubuntu-server:~# service apache2 reload
* Reloading web server apache2 *
* The apache2 configtest failed. Not doing anything.
Output of config test was:
AH00526: Syntax error on line 2 of /etc/apache2/sites-enabled/000-default.conf:
Unrecognized header format %
Action 'configtest' failed.
The Apache error log may have more information.