Debs and Rpms are fine for configuring the machine, as soon as you have it where machines and application services aren't a 1:1 relationship that will lead you in the direction of dependency hell. As each application will want slightly different versions you'd have to be very careful which version you installed.

You can cheat a little. For example I am using some system debs for python packages, but if there were more than a handful of python utility packages that can get unmanageable fast. That leads naturally to the fat jar/virtualenv/static binary approach with manually managed dependencies which gives you isolation between applications, and all the associated costs.