Architecture Guidance: Many off-the-shelf templated sites
I've made an infrastructure close to what you're describing, where we launch sites in 24h after a customer orders it.

Basically the architecture is:


Aegir on a VPS. This allows us to spin up websites, service them, migrate them and sometimes clone them without messing on the server.
An aegir platform with an install profile for our use case
A generic zen subtheme for our use case with a bundle of front-end code
Sweaver CSS for the layout customization of the specific site
A basic features module that is installed by the install profile and multiple optional feature modules with extra views and content types, layouts managed by contexts, that administrators toggle using Feature Sets.
Some additional optional contrib-space modules for things like node access customization


I try to avoid Panels as much as possible because of how much complication it adds. If you absolutely want your users to create fancy layouts, that may be a good choice, but at low price points the users have little tolerance for complicated usage. You might just be creating a lot of failure demand on yourself.

If you're going to just zip up sites, at least give Aegir and site cloning a chance first. You're going to save yourself a lot of work.