Those Circle businesses fund a Chantry operated Circle. They enjoy the privilege of being representatives of the Chantry.
And in this system - they are still connected to the Chantry.
The Chantry receives still benefit from the Circle, and has still some measure of control over the Circle - mages going to war, for example.
They help regulate magic use - among other possible roles.
The Circle has not split from the Chantry in this system - it has been reformed.
Mages are peasants(with the exception of the occasional Connor).
Lets put it another way. There's a Circle in Orlais. They assemble a bunch of wealth. As in the original suggestion, there are no templars on the presmises.
That was never the original suggestion. Templars maintain a presence on circle grounds - but not inside circle buildings beyond those necessary to defend in emergencies.
The Emperor of Orlais chooses to take all that wealth as is his just due, not only are the peasants residing in the tower not paying taxes, they do not answer the draft and are therefore traitors. The Emperor of Orlais attacks the Circle. Since the Chantry has no templars in the Circle, they suffer no casualties. The Orlesians have a more than adequate defence to any Chantry objections. After all, they were only administering punishment to the fullest extent of the law upon Orlesian citizens, and moreover, no representatives of the Chantry were harmed in the process.
I believe you missed my post that stated I'm willing to pay tribute to nations - to crowns that is, not noblity.
The second mages become anything besides part of the Chantry, they lose any claims to neutrality.
I require neutrality in war and international conflicts, and I would think neutrality is best in clashing international politics when possible.
And good thing the Circle is still part of the Chantry.
In terms of the Chantry attempting to chastise any nations after the fact, should that nation attack/slaughter/imprison/enslave mages, there is no political grounding for them to stand on. Mages would not be members of the Chantry, and they would also not be the charges/wards of the Chantry as they are now. They would be subjects of the respective countries and fiefs they were born in, and any interference by the Chantry would be direct interference in the country's internal politics(thus sacrificing the Chantry's own neutrality, which I doubt they'd do for a handful of peasants).
Again - this is a reform and not a separation.