You'd have to ask the author, but I would suggest it is "just in case" no more. Lack of trust that the make file specifies all possible dependencies perhaps. If the makefile were hand-built without automatically generated dependencies, that is entirely possible. Also it is easier to simply advise to rebuild than it is to explain all the situations where it might be necessary or otherwise, which will not be exhaustive.
From the author's point of view, it eliminates a number of possible build consistency errors that are beyond his control so it ensures you don't end up thinking the book is wrong, when it might be something you have done that the author has no control over.
Even with automatically generated dependencies, a project may have dependencies that the makefile or dependency generator does not catch, resource files used for code generation using custom tools for example.
For large projects developed over a long time, some seldom modified modules could well have been compiled with an older version of the tool chain, a clean build ensures everything is compiled and linked with the current tool.
make builds dependencies based on file timestamp; if you have build variants controlled by command-line macros, the make will not determine which dependencies are dependent on such a macro, so when building a different variant (switching from a "debug" to "release" build for example), it is good idea to rebuild all to ensure each module is consistent and compatible.
I would suggest that during a build/debug cycle you use incremental build for development speed as intended, and perform a rebuild for release or if changing some build configuration (such as enabling/disabling floating-point hardware for example or switching to a different processor variant.
If during debug you get results that seem to make no sense, such as breakpoints and code stepping not aligning with the source code, or a crash or behaviour that seems unrelated to some small change you may have made (perhaps that code has not even been executed), sometimes it may be down to a build inconsistency (for a variety of reasons usually with complex builds) and in such cases it is wise to at least eliminate build consistency as a cause by performing a rebuild all.
Certainly if you if you are releasing code to a third-party, such as a customer or for production of some product, you would probably want to perform a clean build just to ensure build consistency. You don't want users reporting bugs you cannot reproduce because the build they have been given is not reproducible.
