The whole point of the documentary is look and follow how this specific transition affects these specific people and their relationships. It's naturally not about universal or idealistic tranny experience like this complainer wants it to be.
1. Trannies use the term "deathname" about their old name and many have tantrums if it comes up. They demand that old records and achievements have to be "fixed" to include their new name and identity regardless how little sense that makes. Bringing up their past self up is seen as dangerously outing them or bullying. Burning clothes and talking about killing their old self is very much on that same track. The mom's grief and old photos are interesting background that shows what's being left into past and how that's affecting people. Just because it doesn't paint the best picture of the tranny doesn't mean it's not fair and informative. As to why the documentary crew was there for that? I imagine that the tranny wanted the burning to be recorded because he thought it was cool so waited on them or it just happened when they were there and picked that moment to show because it was unusual, or it could have been the grews idea to cinematic and they asked for it. Don't know but like I said it seems very tranny approach so I think it was his own doing.
2. She agreed to be a main part of this documentary so it showing her ways of dealing with the situation wouldn't be a surprise to her and them coming with her to work would have needed to prearranged anyway. She didn't get her privacy violated, not unreasonably anyway.
I'm pretty sure your issue isn't that the crew destroyed her "refuge" but that they showed that the girlfriend wasn't happy and that her tranny "girlfriend" was something she wanted escape from and he was causing pain and stress to her even when he wasn't around. As far as the colleagues, of course they are going to wonder about the camera crew, who wouldn't? Also the laughter is appropriate reaction with tone of the anwer. It doesn't matter if he knew about the tranny, the situation was comical regardless of any trannies.
3. That's just what happens with editing, you might get taken out of context or context is shown missleadingly in someway. This can happen even with best and most honest efforts to be fair because whatever is considered important or relevant isn't agreed by everyone. Otherhand showing everything is usually seen as overly long and boring because most people kinda ramble, go off topic, repeat themselves, use filler noices and have long pauses. It would be nice if they also had unedited or at least minimally edited interviews as an extra somewhere to see the context ourselves but might not have been possible for various reasons.
Wasn't showing how the transition is affecting the tranny and people around him the point of this? That means showing what happens, reactions and opinions even if they don't align with the tranny or show him in best of light. Friends have their own lifes and people do get bored with personal drama of others. Nobody likes listening on and on about obsessions about gender issues, especially sinse you aren't allowed say your own options without being called a bigot. The girlfriend was unhappy, they didn't stay together, and him being not seeing it happens all the time as you said yourself.
4. The documentary was about him turning himself in to a woman, what that looks like over time. Of course they are going to document actions taken to make that happen and putting on make up and other vanity stuff is very much about that. Look at tranny message boards, tweets and posts. There are so many my first dress pic, tried out make up, got my own bra everyone, finaly feeling cute naked and so on about their own bodies and looks. This is very much what transitioning is about, not showing it would be disingenuous. The girlfriend wasn't changing herself so nothing about her body image or making her style is shown because it's not relevant on whatever is going on.
5. Well that tends to happen with people who are subject of documentaries. Documentary topics are usually chosen by something it being unusual and unusual things tend to be stressful. Stress tends to elevate bad moments and now you have added weight that will get recorded. It's really not always fun and can make already uncomfortable situation worse but it has nothing inherently do with this relationship not working out. The documentary crew wasn't there 24/7 and going over what happened is what people do in therapy because it helps. I'm not saying doing it front of a camera is same as in privacy of a therapy session, just that opening up about hard times doesn't prevent healing and so cannot be blamed the relationship not working out. Being in the documentary most likely didn't help but it wasn't the main issue at all, that was the transition.
It doesn't matter if partners of those coming out trans might be less likely to stay after watching this. Nor that it might discourage people from transition. It's a documentary following a couple who didn't work out because a large change in their life, that story isn't inherently not worth of telling just because it doesn't paint transitioning as a great thing and trannies worth of stay with the turmoil.