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You'll have to put copies of or symlinks to the files in the include/user folder and then use pun_include in the template.
It's explained a bit here:
http://punbb.org/docs/faq.html#faq3_4

asardar: You might have to manually do the updates to PunBB by hand if they interfere with your changes, but you always have the hdiffs or the patch files to use.

Although it isn't done, that does sound like a bug in your setup

Yann: You would have to implement transactions in the MySQL dblayer

Moved to Troubleshooting, not a bug (the above is the quote from your post)

Nope: install.php doesn't run if config.php exists

Yeah, that looks like a default PunBB install.php file: you can delete it safely

Mostly, any files that don't look right. Be especially wary of anything named system.php

That's the default page you get when config.php doesn't exist/has been messed with (well, the default plus the hacker's message).
I saw that page after you posed this topic. I backwalked the image's URL to a backdoor on another server, which I took the liberty of removing

Wait, was the install.php the default PunBB install.php or something else?

You'll also want to look for any backdoors that might be hidding: check all your folders for files you don't remember uploading there (they might have names like email.php and system.php)

Moved to Troubleshooting
Sounds to me like a mod_security issue. Ask your host to update their mod_security rule

The difficulty of installing a mod is not a good basis for deciding what features to include in the main code base. PunBB is meant to be a smaller, lighter, simpler forum. Adding attachments by default would clash with those goals.

It's still unnecessary bloat

The extension system in 1.3 should solve the problem of tedious mod installations.

I'm not sure: I can't replicate it with FF 1.5