If you have a project that you want to deliver using MSIX from the Microsoft Store and from your own website, you currently must make two AIP projects. The Microsoft Store version of the package must use a Microsoft supplied (ugly) Publisher field and a temporary cert provided by them to match. The version for your own website will want to use a Cert from a Public CA and will have a different Subject/Publisher.
It would be ideal if this could be accomplished with a single AIP project with two builds. This would require the ability to define per-build certificates, and either per-build Publisher fields or just pull from the cert each time.