The USD section in Maya's core preferences exists to store your preferences for USD data in your Maya scene. Within these preferences, you can set defaults to persist across your Maya scene files that consist of USD data.
To find the USD section in the the Preferences Window:
This radio button is also found when you select File > Save As when you have USD data in your Maya scene file in the Save USD Options dialog.
Save the Maya scene file and USD files (recommended): Select this option to save your Maya scene file (.ma, .mb) and your USD files (.usd, .usda, .usdc) to disk respectively.
Save all edits including USD, to the Maya scene file: Select this option to save your current Maya session with in-memory USD edits into a Maya scene file on disk (.ma, .mb). This option serializes your USD edits into your Maya scene file. When you open Maya again, your in-memory USD edits will persist as unsaved data. Important: per layer, any data exceeding the limit of 2GB will not be saved. This option is not recommended as data loss can occur.
Save the Maya scene file only (USD edits will not be saved): Select this option to ignore all USD edits and save only your Maya scene file (.ma, .mb).
Specify your USD save file format in this window. Choose between one of the two following supported file format options:
The following toggles are also found in any Save As or Create option dialogs for your USD data. See Make Path Relative. If you also select Convert All to Relative Paths in the Bulk Save dialog all of the following toggles will be enabled in this window. Setting this preference in this window will save your selection in your Maya scene.
Choose what your colors should display as in the Viewport when in untextured mode. Select from Material Colors (default) or USD Display Colors. Select display colors when working in USD as material colors may be inaccurate from the endless types available (base color, specular color, transmission color, subsurface color, sheen color, coat color and more).