For slotted services, I suggest looking at nix and nixos, a package manager (and a distribution) which pinches some ideas from containers.
As for the main point of your comment:
Yes, native package management is lighter-weight than containers (which is lighter than vms, which is lighter than seperate physical machines). Perhaps unsurprisingly, that weight brings additional features. The main one that containers (upwards) adds is segregation. apt (lovely as it is) can only ensure packages don't conflict on the files that they install - you are on your own for ensuring there are no runtime conflicts. Yes, with proper user creation + management you can restrict their ability to tread on each other's toes (hope there are no setuid programs in there), but that is all more effort than the 'their filesystems are seperate' that the heavier options give you.
There is also the question of tidying up / migrating. Let's say I install number of packages for some thing I'm deploying on a box. After a while I realise the load is too high and decide to migrate one/some of the apps to another machine. apt, etc can tell me what files a package has installed. It can't tell me what files a package has created while running. I'll have to go around and figure out the data (config, user config, log, etc) file locations and probably miss a couple and end up just duplicating the original machine. Or I copy the container file and the half a dozen images that make it up.
It's true that docker (and to a lesser extent vagrant et al) are perhaps suffering from over-use as the are 'the new hotness', but that's because we have a new tool and haven't yet fully figured out how to use it - it's somewhat inevitable behaviour. And yes, for some applications package management is fine and containers is unneeded overhead. But for others it isn't.