There's your problem. Docker adds indirection on storage, networking, etc., and also makes upgrades difficult as you have to either rebuild the container, or rely on others to do so to get security and other updates.
If you stick to things that can be deployed as an upstream OS vendor package, or as a single binary (go-based projects frequently do this), you'll likely have a better time in the long run.
There's your problem. Docker adds indirection on storage, networking, etc., and also makes upgrades difficult as you have to either rebuild the container, or rely on others to do so to get security and other updates.
If you stick to things that can be deployed as an upstream OS vendor package, or as a single binary (go-based projects frequently do this), you'll likely have a better time in the long run.