Personally I don't really see why following some quite common work schedule like 8:30 - 16:30 and having daily stand-up meetings destroy morale. Of course depends on the details, but my life has always been quite nice following standard work styles. Time tracking is a chore that not many like, but still it takes in my experience only 15 minutes or so from the daily time and IMO produces pretty good value.
The issue that many developers have with time tracking is that it requires you to either translate your work into management speak in order to appease the management, or write what you're actually doing and have tons and tons of small blocks in your time tracker that make you look like you're being unproductive and trying to obscure something. Both options add unnecessary mental overhead and interrupt any possibility of having a "flow state".
Writing code and working on software is not a linear process, so writing "worked on feature X" for your entire morning may be accurate, but it's not fine grained enough for what the managers want to see and it doesn't really serve any purpose at that point when you already have daily stand-ups and sprint meetings every week.
This likely isn't the case at all companies and with all managers, but I suspect many have the same experience I've described.