Well, I'm glad you enjoyed yourself! You should have posted in the forum thread: unformatted Youtube walls of text are a pain to read. I agree with the vast majority of your points: they weren't problems in my original imagining of the map but engine limitations meant I had to come up with workarounds.
The gold crates being moved one by one is one example, but actually because they are targeted by the chain of entities that teleport the stacked models, give you loot and teleport your held version by name. The first crate is called goldcrate1, the second goldcrate2 and so on, meaning that I couldn't have them appear piled up on the cart because putting the fourth one in first would have it floating at the back rather than stacked neatly. That's why the bags are fine but the crates aren't: they don't stack. I didn't want to just have the boxes vanish either, so that was a compromise.
The alternate loot drop is essential, really. In the inspirational PAYDAY mission, you end up having to walk through the entire mission while being shot at if you neglect to buy an alternative loot drop, and it's far bigger than this. I wanted to make the favor system properly useful in some regards, so I made the mission a real pain to 100% without the loot drop and some things impossible to find without hints.
I've updated the manager's safe note since, making it clear that it's somewhere on the dullest painting in the room. I still didn't want to make the button easily visible because it makes little sense for it to be in plain view. It's still a cruel place to put it, but it's intentional and isn't anywhere near as evil as it could be.
With regards to difficulty, it really killed me to make the map easier than I wanted but, as you said, it's intended to be the first of many in a campaign, and as such small and simple. To be honest it began as a tech demo for the favor shop but I'd been itching to make a bank heist too and so put it to good use in a tiny one I built in a fortnight. I made that briefing about five minutes before release too, hence the thoroughly mediocre writing. The second one is being worked on and is far more difficult already. By the final mission I imagine a lot of people will be complaining about the difficulty of it rather than the lack thereof.
You mentioned that the loot is meaningless, which is true for the time being but come the second mission you'll find each 1000 loot being translated into one favor for the second mission. Considering that they change the mission in major ways, it may be that the loot ends up more useful than in Thiaf, here's hoping. I may have missed a few points but there were a fair few to try and remember, so good job on putting out some commentary with proper discussion in it!