As a new user, I found the "Saving Tag Changes" message a little disconcerting. If it's not anticipated based on what I've been doing, my natural response (yes, I talk to my computer) is "What are you doing to my files?!" But when I think about it, I realize a program like this is doing hundreds of different things, many of which might result in files being modified. If I see a message like this, it's only because the developers thought it would be helpful. They have no interest in throwing me into a panic. And there's obviously many more processes going on that I'm not being informed of. It's pointless for me to attempt to monitor those and kill the anything that causes me concern.
The learning curve is steep, but I've tried to take responsibility for studying the configuration options and set them to get the result I want. So, for example, all of my music files have already been analyzed and have a replay gain recorded in their tags. When I see an "analyze audio" option, I'm not sure what it does, but it seems prudent to turn it off. Beyond that, I have a lot of meticulously compiled information stored in my ID3 tags. I'm not sure what MC might do to those, but I've consciously taken the risk. So far, I see no indication MC is messing with my information. I note it has added some extended tags. I take this as a sign the developers are well-aware of the issues involved, and perhaps the risk to my precious data is less than I thought it might be.
Suggestions to "chill" and "trust me" are difficult to take (yes, they've been directed at me, and I probably deserved it). But I believe underlying those words is a desire that developer and user find a level of understanding and trust with one another that communication is effective and helpful.