I have no problem with the guides changing plans on the fly dependent on the conditions. I'm sure we all actually prefer them to when it comes down to it. Nor do I take issue with their formal qualifications, or lack thereof. In fact, like many boats in the area, I don't see anywhere on their website that refers to their staff as "divemasters", "DM's", or "instructors"... It simply refers to them as "staff" or "guides". It does say they are all trained in primary first aid and secondary care. Luckily, nobody had to test that statement.
That being said, where I would take issue is the apparently lack of maintenance and the way the situation was handled. As previously stated, the exhaust issue could have been VERY serious. Yes, stuff breaks on a boat, I get that. But, if things went down like the OP said, the staff clearly didn't handle things right. And considering how shotty the air fills and room roof maintenance clearly was, there is a good chance this could have been avoided with proper maintenance.
If the roof leaks that bad, I'm sure it's not the first time it happened, and I would think that is something that could/should have been taken care of between trips... Especially on a boat that prides themself on luxury.
My main issue is with the tank fills. In your opinion, the difference between 21-24 is negligible, but what about the people using those tanks to calibrate their Nitrox from? That is a huge problem, IMO. Every place I have ever dove Nitrox REQUIRES you to check your Nitrox mix before every dive as a safety precaution (as well as to cover their asses from a liability standpoint by having you initial it). This is the polar opposite end of the spectrum.