The Linux filesystem is designed to be more flexible. I would actually suggest this (fragmented) as a backup strategy not only because it saves you a lot of bandwidth and storage space, but as long as you know what to do, restoring the data can often be a bit faster, assuming that you can restore to a base image and layer on your old data.
Of course such a strategy costs time and effort through planning and implementation. There are one-click whole-system backup solutions that take all the brain work out of the problem.
So you do have to address this on a case by case scenario. If you can live without a full configuration (ie you're happy to reconfigure), you can forget all about packages and
/etc/ and just grab
/home/. You could even slice that down and only grab elements of the home dirs. Scaling up you can grab lists of what packages are installed, their configuration, their data all the way up to the entire filesystem.
Just weigh up how confident you think you'll be if the worst happens and you need to restore the system. If you think you'll struggle trying to superimpose a partial backup, just set aside a few extra gigabytes and do full backups. If this is for a server, where regular, atomic backups are needed and bandwidth and storage is premium, you'll have to get a bit more familiar with the tools of the trade.