Command line reference should clarify which flags can be used in a transition

### Page link:

https://bazel.build/reference/command-line-reference

### Problem description (include actual vs expected text, if applicable):

The list of flags fails to communicate which flags are part of the [build configuration](https://cs.opensource.google/bazel/bazel/+/master:src/main/java/com/google/devtools/build/lib/analysis/config/BuildConfigurationValue.java) (because they are part of a [configuration fragment](https://cs.opensource.google/bazel/bazel/+/master:src/main/java/com/google/devtools/build/lib/analysis/config/FragmentOptions.java)) and which are not. This makes it unclear to users what can be [changed in a configuration transition](https://bazel.build/extending/config#user-defined-transitions).

### Where do you see this issue? (include link to specific section of the page, if applicable)

_No response_

### Any other information you'd like to share?

_No response_

Start with the command-line reference page and compare its flag list with BuildConfigurationValue.java and FragmentOptions.java, then read the user-defined transitions documentation. Determine how the reference should distinguish flags belonging to configuration fragments from those that do not. Done means the page clearly indicates which flags can be changed in a configuration transition.

Written by the indexing model from the issue text.