I haven’t implemented anything yet, but the only solution I can currently think of is always including the Section, but having the logic of wherever it displays or not inside the section code. So the section will always be included, but may not neccessarily display.
My alternative approach for smaller sections within the header/footer will be to have them as static sections in the Template, but to actually load them via Ajax as seen here: https://shopify.dev/api/section-rendering . Will be a good technique for smaller secitons needed in multiple areas, e.g. a Store Switcher (drop down of international stores to choose from).