Spoilers for Season 7 and Season 6 beyond this point. Please do not scroll if you haven't watched them yet. As the whole question is spoilersome, I won't be using spoiler tags.
Daenerys was predisposed to accept Ironborn independence in S06E09:
Daenerys: You've brought us 100 ships from the Iron Fleet with men to sail them. In return, I expect you want me to support your claim to the throne of the Iron Islands?
Theon: He [Euron] murdered our father and would have murdered us. He'll murder you as soon as you have what he wants. The Seven Kingdoms. All of them.
Dany: And you don't want the Seven Kingdoms?
Yara: Your ancestors defeated ours and took the Iron Islands. We ask you to give them back.
Dany: And that's all?
Yara: We'd like you to help us murder an uncle or two who don't think a woman's fit to rule.
Tyrion: What if everyone starts demanding their independence?
Dany: She's not demanding, she's asking. The others are free to ask as well.
So at that point, she appeared to be willing to accept secession of individual Kingdoms from Iron Throne.
To be fair she did ask the Greyjoys this:
You will support my claim as queen of the Seven Kingdoms and respect the integrity of the Seven Kingdoms. No more reaving, roving, raiding, or raping.
Which is kind of vague and open to interpretations (Something which good diplomats always keep an eye out for while conducting negotiations).
If some clause or condition is open to interpretations, that often leads to break down in negotiations e.g. IRL in Prelude to Crimean war, a treaty proposed by Great Powers to reduce threat of war between Ottoman Empire and Russian Empire was rejected by Ottomans as some clauses were vague and open to varying interpretations.
So If Yara is supposed to accept her as Queen of the Seven Kingdoms and respect the integrity of the Seven Kingdoms, she can't bloody well secede, can she? And while Daenerys said others were free to ask as well, she never said that she will allow them.
In S07E02 We see:
Tyrion: I can't speak to prophecies or visions in the flames, but I like Jon Snow and I trusted him. And I am an excellent judge of character. If he does rule the North, he would make a valuable ally. The Lannisters executed his father and conspired to murder his brother. Jon Snow has even more reason to hate Cersei than you do.
Daenerys: Very well. Send a raven north. Tell Jon Snow that his queen invites him to come to Dragonstone and bend the knee.
Here she is not even willing to view him as an ally, she wants him to bend the knee and be her subject, contrary to her earlier position re the Ironborn.
In S0703 She said:
Tyrion: Pledge your sword to her cause.
Jon: And why would I do that? I mean no offense, Your Grace, but I don't know you. As far as I can tell, your claim to the throne rests entirely on your father's name, and my own father fought to overthrow the Mad King. The lords of the North placed their trust in me to lead them, and I will continue to do so as well as I can.
Daenerys: That's fair. It's also fair to point out that I'm the rightful Queen of the Seven Kingdoms. By declaring yourself king of the northernmost kingdom, you are in open rebellion.
Isles and Rivers (Later both were separated into Iron Islands and Riverlands) was one of the 7 Kingdoms Aegon the Conqueror took. So what about the westernmost Kingdom? What gives?
Why be prepared to let the Iron-Islands secede but pressure the Northmen to accept her as Queen? If Torrhen Stark swore a vow to be subject to Aegon the Conqueror and his heirs and successors, so did Vickon Greyjoy. Was she just fooling the Greyjoys with vaguely worded promises?