If the only thing you are storing in the database is the XML data, what is to stop you from storing the file directly on the filesystem and bypassing the overhead of querying the database for the single field?
If backups are your concern, there are methods to backup a directory as well.
Usage of MySQL (or other RDBMS) implies there is a relational aspect to the data you are storing. If there's no relationship, this is probably not the tool you are looking for.
Store the data in flat text files which are uniquely named based on each system, not in a database.
Databases (particularly relational ones) excel at storing data in tables with a consistant schema, relating those tables to one another and querying them in arbitrary ways. What you are describing is (based on my reading) basically a web page to display text files. There is only one way to access the data (via what is effectively a unique key, the system name), there don't appear to be any relationships, and the data will vary considerably from system to system (hence your issue with lots of columns).
So I don't see much benefit in using a relational database (a document database such as RavenDB, CouchDB or MongoDB may be a better fit, but even they are likely to be overkill for what you describe).
If you're really keen on using MySQL, just store the contends of the file in a table you can lookup via a name:
system_name varchar(255) NOT NULL Primary Key
file_type char(2) NOT NULL = 'F' or 'IF' (for frequent or infrequent)
data Longtext NULL
And parse your textual data in PHP (or simply display it).
You could store your data exactly as you receive it, or process it into XML, JSON or YAML to standardise it.
I just noticed the show common properties requirement.
Perhaps you could have columns in your table for those common properties, but not all the properties. You can quickly query the common properties while still being able to view the full data. (I don't have direct experience with any of the above document databases, but I believe all of them will let you index arbitrary fields in your documents, which will be much more flexible than a fixed number of columns).
If you really want to stay with MySQL, you may want to look into the Entity-Attribute-Value pattern. (IMO, EAV is an anti-pattern, but it should be OK just for the common properties).
Of course, if display time isn't really a big worry, just opening and parsing 1000 text files isn't going to take too long (I'd expect ~10 seconds).
Best Answer
From your comments, one solution might be to make a Master-Slave replication setup (link to mysql replication here)
I would make the backend the Master, and the front-end the slave. If your front-end needs to write (contact forms, tracking etc) you would update your code in the Front-end to read from the slave, and write to the master.
The downside is, depending on the load, your backend-writes might be delayed a few seconds or more. But as an anecdote, I've got a server that handles 120 commands /second (averaged, as reported by munin) and the slave server isn't behind by more than 3 seconds.