Please clarify "Saving the post title to the custom table will lead to some unexpected issues." If this is a bad idea, I won't do it, but I'd like to know more about your concern.
Regarding the content: Yes, creating alternative/replacement fields to use in place of the native WP content has indeed been the strategy thus far. The reason I asked the above, however, is that I wanted to keep the Gutenberg functionality for the main content on the CPT page.
Is there a way to load Gutenberg into a Metabox-generated field that is saving to a Custom Table?