Hooks

The simple solution to the above problem is hooks
Every driver that would not be pulled-on by the linker has a hook symbol
Some relevant code refers to the hook (main, or setup.c)
We waste at least one byte per driver, but it may be acceptable

By referring to the hook, you claim your need for the code

  if (CONFIG_HAS_USB || CONFIG_PLL_CPU > 1)
        pll_hook = 1;

A more structured operating system may be hook-based
If drivers have standard operations and you open them by name
You would implement an "import" or "use" mechanism like this

This is what BertOS was doing, for example
It is a library-based OS building multiple applications
Each application requests its own feature-set
Then, the match at run-time is name-based