I'm not a WordPress user. I used it once and chose not to use it again. I've used ProcessWire for my past seven or eight sites.

Soo ...

It sounds to me (based on the above few comments) that there are right AND wrong ways to cut up and organize your WordPress templates.
In ProcessWire, there is no wrong way. There is no right way.
You can use a php include for a header. Another php include for the footer. And combine your templates as YOU see fit.
Or you can go the advanced method and follow a Ruby-escue method and chop your templates up and follow a MVC technique.

Again, it's been said by many other users of ProcessWire: totally custom. Your way.