https://www.youtube.com/watch?v=DKutw1zDgms
Convinced that the primitive races of the Horde can help them achieve victory over their enemies, the Forsaken have entered an alliance of convenience with the savage orcs and the proud tauren. Harboring no true loyalty for their new allies, they will go to any lengths to ensure their dark plans come to fruition.
And from them, derived the position BEs had within the Horde. As Sylvanas was all to willing to remind LTT:
http://media.blizzard.com/wow/lore/pdfdownload/leader-story/lorthemar-theron/lorthemar-theron-enUS.pdf
"For a while now my people have stood guard in these lands, and it is by my hand that you have any place within the Horde. You will aid us in Northrend, or I shall cease to aid you in Quel’Thalas."
[…]
“You heard her, Rommath,” Lor’themar interrupted. “We go to Northrend or we lose Forsaken support—and likely the rest of the Horde’s as well. So we go.” He turned to leave again.
Its rather clear Forsaken and BEs didn’t kickstart their relation with the Horde as in swearing absolute fealty to it’s leader. Which would be natural, given the cultural differences that marked them apart from Troll, orc or tauren mindset.
They had their ruling bodies, and only dealt with Horde affairs for as long as they either felt obliged to (BE), or had some additional interest in mind (Forsaken).
The ultimatum given by the Zandalari about them keeping their own ruling system, is in no way different to the one the Forsaken initially had, that had them tagging along the Horde for as long as it worked on their favour. Or much like BEs under LTT, that came into the fold because they incurred into a life debt with Sylvanas and the Forsaken.
Much like LTT tried to do, and would’ve done, regarding the war against Malygos? Like the Forsaken did with the onslaught in Northrend, when they sent their own forces independently from the rest of the faction ones?
I’ll repeat, that all this story about some “rebel” faction member that plays its own game, i’ve already seen it in several other Horde races. Yeah, the Zandalari aren’t the first one that enter pumping their chest proclaiming how independent they are.
But still, given ingame mechanics, writers plots, and an overall need to encase each race under a blue or red banner, those postures have never lasted.
There won’t be a third faction. And the Zandalari are about as “independent” as the Forsaken, or BEs thought they were, when both were first introduced.