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For point 2) you can add those into gnome-session-properties , to start when there is a system startup. It should work

Regarding case 1, I am not sure why its not picked, for me I have custom changes in .bash_profile and it does reflect when I log out and log in back again.

Also can you try to check /etc/profile or .bashrc and put your changes there and check if it gets picked up or not ? Also is there a .bash_profile call from your .bashrc ?

For further customization of Gnome3 check the above links mentioned by @bodhi.zazen Also check the link from Archwiki regarding Gnome3

Also GNOME3 now has its official extensions website Any customization to Gnome3 is a cakewalk and super easy.