Is there any reason to store my data in /var/?

Solution 1:

There's more than enough reasons not to do this. Here's a couple:

1. It's rather opaque for the guy that comes after you, and as it is non-standard.

2. It violates the FHS

3. It will mess up things like Selinux and AppArmor by not adhering to conventions. You will either need to write your own policy or disable Selinux and AppArmor all together.

4. After updates to packages that alter configuration files to a new format or to have new features, you will have a relatively hard time porting your changes to the new configuration file.

Backing up to your servers important information can be just as easily done by backing up /etc and /var in their intirity.

Solution 2:

If you configure all your apps to find config files and store information in /data/ and they works properly, i don't see any negative side.