Pushing capabilities and role_list to sub-sites works awesome, pushing menu... not so much. Each site does not use the same exact plugins so what I did was enabled all plugins for the main site, went to the network admin and set the options in the main menu tab, the roles and the capabilities tab and then saved. Went to configpress and turned on apply_all with the following options:
multisite.apply = "capabilities" multisite.apply = "role_list" multisite.apply = "menu"
Am I missing something?