While talking to Barry Kooij about how he sells his products, I discovered that he and Mike Jolley worked together to make LicenseWP, an alternative licensing plugin to WooCommerce’s official Software Add-on. It has a couple advantages, one of which is the ability to use a single license key for multiple products — enabling simple bundle functionality. You can also use licenses with variations.
The extension — though only on Github — is used on WP Job Manager and by Barry for Never5 products, so is likely to stay up to date, if you need similar functionality.