@PNJ @darrenhillconsulting @karlenigma We had faced this issue as well.. And only once you consider @PNJ comment does it make sense.
Could one theoretically create a SuiteApp with the same app/publisher ID as an installed SuiteApp, add a hiding.xml and locking.xml (set to UNHIDE & UNLOCK) and then deploy? Obviously the SuiteBundler required a login to the Deployment account to unlock/unhide components, whereas (I don't think) that anything blocks Eclipse from creating an SDF project with another publishers Id....