Changing the VisualEditorNamespaces config (wgVisualEditorNamespaces) is currently required to use VisualEditor with Flow. However, this has other undesired side effects, such as marking VE available in ve.init.mw.ViewPageTarget.init.js.
Also, if Flow were not enabled on certain pages in that namespace, normal VE would then be enabled there, which is undesirable.
There should be a way for us to use the API (or certain safe parts of it, such as 'parsefragment') in certain namespaces without the other side effects.