As you work on these projects, I do think you should submit your code changes to Joe Audette for consideration. If they are focused, well done, and do not negatively impact existing mojoPortal sites (i.e. all changes are fully-backward compatible, and the upgrade process will not require users to make configuration changes in order to keep using their sites as-is), I'm pretty sure that Joe will give fair consideration to incorporating them into the mojoPortal core. I speak from experience on this, having just made some changes to allow fallback LDAP authentication that will benefit our site and others who want to work the way we do. Having your changes incorporated into the core will also benefit you tremendously, since you won't be left maintaining a dead-end code fork. Since you are so security-conscious, I'm sure you can appreciate how important it is to be able to upgrade as soon as possible when security issues are discovered.
Changes to obscure the CMS type are not very compelling to me, since part of how we give back to mojoPortal is by leaving the "powered by" link on our sites. But I would definitely be interested in seeing what you can come up with for an installation wizard (and hopefully a companion upgrade wizard, since mojoPortal upgrades happen quite often). It would be very nice to have an easier way to manage all of the user.config/web.config keys. And I would find improvements to the search quite welcome as well.
About the community comment, I'll try not to take offense, but you should know that mojoPortal is a bit different than a lot of other open source projects--Joe has literally dedicated his life to this project, now that it is his sole source of income (from add on products, etc.).
Jamie