I truly think, in this case, it's a simple matter of there being a bug somewhere in the ecosystem. If I had to guess where it is, having all the information I have to date, is that when I enable iCloud on my iPhone, it should move my notes there into the cloud.
I don't think it's a bug (ergo, I don't think it's something that will get "fixed"), I think it's by design with the move to an integrated account-centric information structure across all of the ML apps designed to allow the segregation of personal information into segments that should be shared and segments that the user doesn't want shared as well as being able to segregate into various user accounts. [I think most of us, because of the manner in which it evolved tended to think of iCloud as just another way to sync information between our devices, but ML makes pretty clear that you have to think of iCloud as your personal server with accounts such as "On My Mac" or "On My iPhone" being files you expressly don't want to share on the server...sort of like at work where you might store all your work docs on theworkgroup server, but would want to keep your personal files just on your own local device. A clear distinction between syncing and backing up
Mobile devices, with their more limited capacity allow you to make these information choices, but don't allow you to manipulate them on the back end - that you have to do on your desktop or via iCloud.com (note that on your mobile devices you can't even sign into iCloud.com on Safri... you're limited to the capabilities of the mobile app).
I'm with you in that there definitely should have been some "Before you install information provided which should have alerted you to the fact that information which you had designated as local" on your mobile devices, and was previously sync'd to the REMINDERS category, needed to be moved to an On My Mac category to preserve its accessibility in the Notes app.
There are already a lot of third-party utilities that enable you to move data from your phone to the Mac (search on CNET... I think most were designed for playlists and music files, but there are some broader ones) If they won't currently handle notes, I would bet that before too long you will see some of them upgraded or new ones that which will enable you to move your On My iPhone data directly to your Mac.