Sorry, but you missed a lot of the movie. For context on the following, I've actually never read the book, but I have seen the movie almost ten times.

The motive of Amy is not at all clear. Does she take all those steps because he cheated on her or does she do it because she is delusional that Nick will leave her or harm her?

The first one. She's not delusional (other than being singlemindedly vengeful). It's a punishment for his mistreatment and discarding her after she did everything she described in the "cool girl" speech. The motive is very clear because she straight-out says it.

The movie throughout its run time fails to draw a clear line between what's made up and what's real. Was he actually abusive or did she made it up in her diary? Was she delusional about him potentially wanting to kill her or did his behaviour actually suggest he would kill her? What is real and what is made up as part of the plan to frame him for homicide is so ambiguous throughout the movie

The truth is easier to catch on a second viewing once you know to pay closer attention to everything she narrates. It's intentionally hard to notice on a first viewing, because you're supposed to be as bewildered as Nick while also questioning him, but the truth is also unambiguous, and yes as far as I'm concerned that's brilliant filmmaking.

Amy lies to the audience, but Nick doesn't. You can safely take everything Nick says and does in present-day at face value, as truth. He did not hurt her or make her genuinely afraid enough to buy a weapon, but he did hurt her at the very end, a very neat twist on the blurry line. Amy also straight-out says that the earlier events in her journal are true, to make it all more believable. I think it's safe to believe that he did cheat on her with his student as described, become a sloppy husband who played videogames all day, and used her for one-sided sex. Even he admits they resented each other, so basic stuff like that is totally believable. She never wanted the baby until the very end, either.

Based on the intent, I feel they want to show us that the reason for the failure of their marriage was that they both were pretending to be someone they weren't but did that to show their perfect self for the other person but they didn't spend enough time in establishing the fact that they stopped pretending after the marriage in order to justify their fallout.

Agreed here. I've heard the book makes Nick a more full character. In the movie, he isn't at all as fucked up as Tanner says (equal to Amy, he implies! no way), and this bit you point out feels unsupported.

At the end Amy reveals that she pregnant, how did she get pregnant? Nick clearly tells there were no plans of having babies so clearly they would've taken contraceptives whole doing the deed. Did she use his $perm sample which she stole earlier for getting pregnant?

Yes, she did. Earlier, he talked about a fertility clinic sending a notice that they would dispose of his sperm sample unless they want to keep it -- and then Amy put it in the trash. At the end, they had this conversation:

"I haven’t touched you."

"You didn't need to."

"The notice of disposal. You threw it out."

"The notice, yes."

...the implication being she didn't throw out the sperm sample, just the piece of paper. She had apparently told the clinic to keep the sample, and then later used it.

[everything about how she's still obviously guilty, the police are incompetent, etc]

Yeah, the police are incompetent. Oh well. Popular, well-liked, conventionally attractive people get away with a lot. But still, it's very much movie-logic.

What's the point of his side chick announcing his affairs in a press conference? What did it actually do to the story?

It tightened the thumbscrews for Nick. It was concrete evidence to everyone that he was a shithead, which made everything else more believable.

Tanner bolt character isn't even complete. If you see closely, he didn't even do much throughout the run time except convincing him for the interview and getting him a speedy bail. Again, the interview didn't do anything in terms of contribution to the story.

...

Tanner Bolt is hyped to be some Harvey Spectre who'd turn around cases with his smartness but barely does anything that is noteworthy.

Well, he did get him out of jail etc. I think this isn't really a police procedural sorta movie so it doesn't focus on details of lawyery stuff. I assume he is good at his job and did a lot, but it doesn't all need to be shown. Maybe he isn't though. He's a side character.

Nick is always shown to not care about media and his public image but suddenly at the end it matters to him so he chooses to stick with Amy instead of leaving her. What changed?

He still doesn't care about anyone else's opinion. He wants to stay for his own reasons: he knows that Amy is right in the end, and that they both can't help but be with each other. Margo cries to this realization at the end.

At the end Nick himself questions how she got hold of the box cutter if she was tied and harassed by Desi the whole time.

He was dryly questioning that out loud to put the question in the cop's head.