Godmother's assumptions?

Okay, let me break this down as best I can.

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She assumed that Prince Charming would be the one to rescue Fiona, which we know didn't happen, considering the first film.

Correct. Harold even calls her out on it:

HAROLD: It's not my fault; he didn't get there in time!

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If Shrek hadn't come along, some other knight could've eventually rescued her.

I'm less convinced about this one. I'd argue that it was reasonable for her to assume that nobody else would be capable of rescuing Fiona. We see that plenty of people had already tried to rescue Fiona prior to Shrek coming along, and all of them had failed, quite painfully.

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She also assumed that Charming would be Fiona's one true love if he was the one to rescue her. There would be no guarantee of that either.

Correct again. But I don't think she assumed that at all. I don't think she even cared how Fiona felt. If it turned out Fiona didn't love Charming - which she didn't - she was prepared to drug Fiona with a potion that would force her to love him:

FAIRY GODMOTHER: Have her drink this [potion] and she will fall in love with the first person she kisses, which will be Charming.

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Godmother put the spell on Fiona to keep her changing into an ogre every night as a secondary precaution to keep her in the tower

Wrong. The ogre-transformation spell was cast on Fiona by a witch, and was the reason she was put in the tower in the first place. There is no canon evidence that the Fairy Godmother had any involvement in that.

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Since he's not her true love, he'd have rescued her and she'd still turn into an ogre every night.

Correct, but it's likely in that scenario that the Fairy Godmother would have used a spell or potion or something to reverse the spell. After all, she quite fervently believes that:

FAIRY GODMOTHER: Ogres don't live happily-ever-after!

...which, by the way, is another incorrect assumption of hers. They can, and do.

I don't believe it was just assumptions but rather careful planning to rig things in her's and Charming's favor, which ultimately was undone by one person....Farquaad.

At the end of the first movie when Fiona and Shrek kiss and the curse is broken, Fiona is surprised that she remains as an Ogre (though in Shrek's eyes she's still beautiful). This is also shown in the second movie where Fiona's parents, Harold and Lillian, as shocked that she is on Ogre. This would suggest that Fiona's "curse" didn't exists before she was locked up

I suspect that the Fairy Godmother did curse Fiona before locking her up and that when the curse is broken Fiona's form would match her True Love's, choosing Fiona's Ogre Form to deter anyone else from saving her since the Magic Mirror was going to warn Farquaad about it and we see his reaction at their wedding so one can assume that had Farquaad known about the curse me might have chosen someone else.

this way when Charming comes along, knowing full well about Fiona's curse and the form she will take will match his. Also we see that in the opening for someone who's about to save a princess from the dragon he just mentions in his monologue he's awfully calm, even taking off his helmet and getting his mouth spray out. To me this stinks of fowl play and that something was in place so that Charming wouldn't need to fight Dragon, or atleast properly so it would mean that she was set up as another means to deter anyone else other than Charming, evident by the fallen knights Shrek and Donkey saw.

Considering also that Shrek and Donkey just walked to where Fiona is without any difficulty and took I think a a day or two (I only recall 2 nights that they camped out on the trip back and that was because Fiona wanted to stop) we can probably assume that Duloc is far far away from the Kingdom of Far Far Away. I believe this too was another part of her plan. Since Duloc was the closest kingdom it would stand to reason that Fiona's heroic knight would more likely come from there and we've seen the quality of the knights (all the best knights got their butts handed to them by an Ogre and a Donkey) and there didn't seem to be any concern from anyone else outside Duloc from Farquaad's rounding up of Fairytail Characters.

Also with the Potion "Happily Ever After" Fiona too was affected and like Shrek to make the change permanent she must kiss her true love by midnight (remember what the girl's were suggesting to Shrek how they would be his True Love). But the plan was to make her fall in love with Charming using a love potion which would cause her to fall in love him when they kissed. This means the Love Potion would have to be able to change who Fiona's True love is and set it to Charming. I wonder now what was in that mouth spray Charming used when he arrived to save Fiona because I don't think his mother would have left it to chance that Fiona's time alone might have made her bitter to Charming for taking so long.

This careful plan however was foiled by Farquaad's desire to be a proper King which the Magic Mirror pointed out that he needed a Queen. he wouldn't go himself so he planned to send someone else. as luck would have it Shrek only came to get his swamp back at the time a Champion was to be chosen to get her, thanks in part to Farquaad's policy making all the Fairytale Creatures uses his swamp as a refuge. so while Fairy Godmother and Charming could blame Shrek it was in fact Farquaad who screwed up her plans.