I added that option now (github master
https://github.com/Flyspray/flyspray/commit/7543e7afc07129535cb88191726b834f2c65b049 ) also for the global settings.
Go to global prefs ?do=admin&area=prefs#general and set 'Default Project' to 'All Projects''.
Go to 'look and feel tab' ?do=admin&area=prefs#lookandfeel and set 'Default entry page' to 'Top level view'.
(maybe need some review what of the global prefs setttings should be grouped together in which tab)
There is a little(maybe weird) logic involved like when there is only 1 project (exists or visible for the current user, depends on some permissions too ) when and what top navigation elements are visible.