Hi kt1974,
I can probably provide sensible answers to some of those questions if you can copy and paste your journey history in a reply. Without specifics I can’t really help.
Will I get in trouble for all my theoretically Incomplete Journeys?
It depends. If you touch in within your zones and have a ticket covering your journey beyond your zones then, no. I really need specifics of journeys made, touches made and other tickets held.
Will TfL ever untangle the fare mess?
They’d love to untangle it, you need to lobby your MP.
Will we be allowed to buy Boundary Zone tickets online or at (all) machines?
Online is already possible by using https://tickets.railforums.co.uk and use the Advanced options to say what kind of travelcard you have.
Will the whole South East ever be Oyster-compatible?
No.
Will the absurdity of different fares and different definitions of off-peak depending on which gates you use at the same station ever be untangled?
Can you expand with an example or examples and I’ll try to answer.