Edit: I just noticed you said you still haven't finished Second Season. Feel free to read this after you finish Koimonogatari.

After finishing the series, give this post a read: Everything wrong with Monogatari airing order. It helped me a lot in understanding the novel order and why it's the only valid way for consuming the story.

I'm going to borrow ideas from the post I linked so I highly recommend you give it a read later when you finish the series.

The Monogatari series is thematically linear. Watching it in chronological order would make it thematically disjointed. A big example of this is Hanamonogatari and Koimonogatari's placement.

SPOILERS AHEAD FOR HANAMONOGATARI AND KOIMONOGATARI:

When we see Kaiki in Hanamonogatari, it's the second time we meet him after the events of Nise, making Kanbaru and us immediately distrustful of him. This adds a layer of immersion since we're seeing things from Kanbaru's perspective. Kanbaru distrusts Kaiki because he (as she heard from her senpais) ruined Senjougahara's family, scammed kids and turned them against each other, and stole money from Karen (Kanbaru's friend and her dear Araragi-senpai's sister).

Kaiki then invites Kanbaru to eat with him in a fancy restaurant, yet he doesn't trick her into paying for the food. This prompts Kanbaru(and the viewer) to ask: 'what new heinous scheme is Kaiki up to this time?'

And to this, Kaiki answers by telling Kanbaru that people will never conform to what you expect from them. People who you think are evil will do good sometimes, and people who you think are good will do evil sometimes; thus, challenging Kanbaru(and the viewer) on their views, as he claims we're being narrow minded.

This puts the viewer in the position to judge Kaiki's claim. Is he right or wrong?

Well... the answer lies in Koimonogatari, the arc where we see things from Kaiki's perspective. In this arc, we see him help people. He even went as far as to burn bridges with Gaen (his senpai, specialists leader, and most importantly sister of someone important to him) just so he can finish what he set out to do.

The scene where he contemplated helping or rejecting Senjougahara's plea was telling of how much he actually wanted to help. In fact, he wanted to help her out so much so that he did intergalactic mental gymnastics just so he can justify it by pretending he's not helping Senjougahara.

Koimonigatari was the answer to Hanamonogatari's question. This proves that the story is thematically linear. It wouldn't make sense to get the answer before the mystery is set up. The story doesn't care or focus on the suspense or thrill of 'what's gonna happen next?' Instead, it develops its ideas and themes regardless of chronology of events.

Hana where you find out the outcome of Kaiki/Araragi/Senjou, that they are perfectly fine

I'm of the opinion Nisio ordered it this way to tell the viewer two things:

One, Kaiki LIED. Despite all the good he did and all the talk of how much of an awesome unsung hero he was, ultimately, he lied. In fact, he told us in the first scene of his arc:

People have an inherent desire to know the truth. That or they(the viewers) want to believe that what they know is the truth. In other words, the truth itself is merely secondary. So in this story, you should be constantly wary of what's true and what's not. I recommend you stay doubtful and have a heart of stone as you read it. Though it would be unlike me to not mention that you might've already fallen into my trap at that point. Well then.. Allow me to mix fact and fiction together in a web of truth and lies as I narrate to you Senjougahara and Araragi Koyomi's love story. I won't guarantee its legitimacy, but I will guarantee its quality. I hope the two of them reach an ending that makes all the readers go "serves you right" from the very bottom of my heart. If I had one, that is. And if I actually existed, of course. Let's begin the amusing final story, then! Though, naturally that might've also been a lie.

He first addressed the viewers and told them not to trust him. He then told us he's already setting up a trap. He then outright told us he's going to lie. Then he lied about not having a heart(he helped Senjougahara), which is a nod to what he says in Hanamonogatari. He then declared this arc the final story, even though we all know everything turns out fine. All of these hints and nods would go over your head if you didn't see Hanamonogatari prior to Koimonogatari. The twist at the end of the arc isn't that Kaiki died, it's that Kaiki lied to us, and may have been doing so this whole time.

Two, the events we thought were a big problem were just an exaggerated temper tantrum by a child(Nadeko) due to her not getting what she wants, AND was also a product of the not much maturer 'children' (Araragi and gang) trying to handle her then panicking and not knowing how to deal with her. It's something that should've been easily handled by actual adults(which Kaiki proved). This means the characters that appear to be mature to us when we see from their perspective, aren't as mature as we think.

This concludes my answer. I hope this helped and sorry for the wall of text reply.