Allow builders to specify the Transforms

Desired workflow
I created the restbuilder extension which recently gained some traction. It is typically used in this workflow:

1. Documentation in reST with Sphinx-specific directives
2. Run Sphinx with this reStructuredText Builder/Writer
3. The result is documentation in reST with only doctree/"vanilla" directives
4. Publish on e.g. GitHub (which understands reST, but not Sphinx-directives).

While refining the extension, I bumped into an issue with substitutions:

• reStructuredText does not support nested markup, like italics in the name of a link, or inline images in a table.
• The workaround is to use substitutions in reStructuredText.
• Sphinx resolves these substitutions with the Substitutions Transform.
• That's an issue, my writer needs the substitutions, not the nested markup.

Feature Request
I like my builder to be able to disable specific Transforms, in this case the Substitutions Transform.

Possible alternative
An alternative is to create a Transform that re-adds these substitutions, and apply them in the Writer (just before the Translator), rather than in the Reader.

Considerations
Currently, Sphinx is sharing doctrees between builders. This already is an issue, as reported in #8974. However, allowing builders to easily add or remove transforms will likely make that problem worse.

Start by reviewing the builder and reader transform lifecycle, then read the shared-doctree concern in issue #8974. Compare disabling the Substitutions Transform with re-adding substitutions later in the writer. Done means builders can control transforms without introducing incorrect shared doctrees.