Etrecheck does not perform any benchmark or speed tests, but it is a good diagnostic tool in today's complex systems. I am wondering why the formatting should be different between the two Etrecheck runs or why the first one (run in normal mode?) is truncated and significant information left out. I also notice the Kernel Extensions report is missing in both listings, it may be you have no kernel extensions, but it would be a very rare system that had none. Whether they are loaded or not EtreCheck identifies the ones present and flags those that are not loaded. The two reports should be pretty much identical with the Safe mode report showing more kernel extensions as (Not Loaded). Try running it again and see if you do not come up with near duplicate listings with the Safe Mode version indicating LaunchAgents and/or LaunchDaemons that are not loading. The missing information and inconsistencies between the two Etrecheck reports makes it difficult to identify any reason for significant differences in performance between normal and Safe mode operation.
Even with the report inconsistencies Etrecheck reveals two notable hardware issues directly related to system speed, Jon has already mentioned the 5400 rpm disk drive and fortunately it can be upgraded. A 240GB SSD runs around $120 and with careful management and the use of iCloud and new iCloud features in Sierra might be enough enough disk capacity. A 480GB SSD runs in the $210 neighborhood. There is no question upgrading to an SSD would make a very noticeable improvement in the tasks you have noted. The other speed limiter is the 2 GHz quad core i7. I am a big fan of the quad core i7 processors but 2 GHz is near the bottom of the i7 food chain and unfortunately it is not upgradeable.
