Concerning the tools, it seems that the current behavior is different from what I thought it would be and what the documentation seems to imply.
In short, on startup ImageJ does not load the tools from the StartupMacros, but from the last configuration (IJPrefs.txt).
Also the first item 'Startup Macros' in the '>>' menu of the Toolbar just seems to load the macros, not the tools from StartupMacros.txt: It loads the tools as they would be at startup, where they come from IJPrefs.txt.
To read the tools from StartupMacros.txt, 'Restore Startup Tools' in the '>>' menu is needed.
Noted by Wayne and Michael Schmid: