I've never killed any of my customers. Ask your surgeon what your odds are in his gifted hands.
I have nearly killed one of my customers though, back when I worked in healthcare. None since I started plumbing though. In fairness, making the plumbing non lethal is a lot easier than healthcare. Hustlers will find a way though.
Here are some thoughts:
I think you're underestimating the price of the boiler. Not sure what unit you're looking at but $4000 seems low rather than high. There is significant material cost in addition to the boiler (though it's a fraction of the boiler), but more importantly everything is going through the usual retail markup.
The swap out may seem relatively straightforward but half a day would be extremely fast for a straight swap. All of these little steps take time and that venting redo is a bunch of extra time beyond a straight swap. And it's unlikely this is a straight swap. Details change over the production cycle. I feel like all the unions installed on water heaters to facilitate an easy change are a bad joke. Little differences take time.
The hourly rate for a bid is higher than time and materials too. The company is taking the risk that this takes longer than expected so they pad the rate to accommodate the fact that some bids go over. But in exchange you get a concrete price rather than a who knows? And mind you that this is a two man job.
I wish I was making $500/hr though. I'm not a union guy but I bet there are some surgeons who are jealous of what a union plumber makes. I remember them griping about Medicaid surgeries where they netted about $25: