This is not just not have ~ expanded into /home/username but also just has other parts of the shell not being executed and I am not sure this was inteded behavior before. For example lxsession-logout --prompt "" when run from a terminal will display no prompt as you are setting the prompt to the empty string will still display the quote marks. also setting the logout command to lxsession-logout --prompt `whoami ` when run from the command line will display your username as the prompt and when set in default apps for lxsession will display the literal value `whoami ` on the prompt for your logout. So I don't think this is just ~ not being expanded and more that all the features of the shell aren't implemented for entries in default apps for lxsession.
This is not just not have ~ expanded into /home/username but also just has other parts of the shell not being executed and I am not sure this was inteded behavior before. For example lxsession-logout --prompt "" when run from a terminal will display no prompt as you are setting the prompt to the empty string will still display the quote marks. also setting the logout command to lxsession-logout --prompt `whoami ` when run from the command line will display your username as the prompt and when set in default apps for lxsession will display the literal value `whoami ` on the prompt for your logout. So I don't think this is just ~ not being expanded and more that all the features of the shell aren't implemented for entries in default apps for lxsession.