Perhaps you're fighting against Scrivener -- expecting it to be one bird when it's really another bird? There are many ways to work with Scrivener in an outliner-style hierarchy of texts -- two of them that might help you are the ability for texts to be children of texts in a nested manner, and "Scrivenings" mode. Section 6.4 of the Manual explains Scrivenings. There is a vibrant and very thoughtful community at the Scrivener forum who can help you sort through using Scrivener a way that meets your needs.

Nhaps wrote

My bottleneck is the lack of outline capability in Scrivener plus the lack of ease for wiki/link creation throughout the document. The outliner is geared for only first and second levels, including a synopsis. It does not go deep enough for paragraph levels, for example. Internal links work only for documents.
But the lack of integration is still there because the outliner is enslaved to the binder, and these work only at the surface of the project.