Hi
PiaF is just Centos with the appropriate dependencies in it including flite, then Asterisk 1.4 installed from source, then FreePBX installed over the top so that mere mortals can configure the system.
So you are welcome to add anything to it, and it should not break anything - and if you do break anything (on a non production system), just re-install - and if you have taken a backup from the FreePBX section, it will not take long to get back to where you were.
Tip for back up and restore:
Back up the whole system via FreePBX and call it "now", then pull down the tar file created from /var/lib/asterisk/backups/now using something like winscp if you are a windows user.
Create the new PBX, then do a backup, again call it "now" so the appropriate directories are created then upload the tar file.
You can then restore what you need to via the FreePBX interface.
A couple of caveats when creating new web interfaces for fax systems or anything which requires a web page etc.
Anything you put in as a FreePBX module in /var/www/admin/modules will not be protected by the database authorisation, so you would need to consider putting it in the maint directory where it is protected by .htaccess (maint /password by default)
You can then create a link to it from the FreePBX interface in the same way that I have created the Configedit / A2Billing Admin / PHPMyAdmin / sysinfo module links You should be able to work out how it has been done by inspection - this just makes it look like it look like a cohesive system.
The issue then is if you need to allow access to users without giving away the top level maintenance passwords.
I would recommend that you create a directory called users, give it the appropriate ownership (chown -R asterisk:asterisk /var/www/html/users) and permsisions then modify the httpd.conf file in /etc/pbx and by inspection you should be able to extend the .htaccess coverage for wwwadmin to your new user directory.
Anytime you edit httpd.conf, just issue the command httpd -k restart to let apache pick up the new settings.
Yours
Joe