Once things settle down, and a regular competition can be established, I think the TT final really should be AUS vs NZL, super bowl style. Indeed, going full mini-NFL seems a fairly logical way to go for me (and probably what they should've done a few years ago when SARU wanted teams everywhere).
Assuming both Island teams get off the ground you'll have an Australian and New Zealand division of six teams each. Each team plays everyone in its own division twice (home and away) and each team in the other division once (alternating venues) for a 16 week regular season, with 8 home matches and 8 away matches. I see the NZ franchises have said they need at least six home matches to break even. I assume that's similar for Australia, so this satisfies that with a little bit more. Not quite sure how the bye's would work in this scenario though. Even numbers mean two teams would have a bye at the same time, and I don't think there would be bye's every round, so some rounds would have one fewer match than normal.
EDIT: Would also be separate points tables across the entire season.
For the post season you could do a straight top two divisional final leading to a TT final, or run it like SRAu did this season. If time permitted I'd prefer the SRAu version. So the total season would look something like this:
Play against all teams within your division twice (10 matches, 5 at home)
Play against all teams within the other division once (6 matches, 3 at home)
Qualifying final: Regular season 2 vs 3 (hosted by 2)
Divisional final: Winner of qualifying final vs 1 (hosted by 1)
Super Rugby TT final: Winner of divisional finals play
If the player/depth disparity ever reaches the situation it did a few seasons ago, or one division simply has a collective shitter of a season, then sure, you potentially may get the odd season where the true final is in the divisional round, but frankly I don't really care. A TT final should be just that, trans-Tasman. A Beldisloe sneak peak. Also, just run with the David vs Goliath buildup in those cases.
Someone mentioned before about shopping the TT final around like they do the super bowl. I'd be on board with this if they could generate enough commercial and fan interest. Though I'd add the caveat that the final needs to alternate between the two countries, and maybe have some sort of mechanism limiting how often a particular city hosts it (assuming you don't want every final to always be in Auckland or Sydney). Even if they can't generate enough commercial interest to shop it around, I think having the TT final location set by the unions a year ahead of each season would be beneficial (and, again, alternating between the two countries).
There's 958 pages in this thread, and several posters who are clearly familiar with the NFL/American sports, so much (probably all) of this has likely been suggested before.