i have this problem now as well, did anyone try to solve the problem without going to db and change it manually?
my solution was to use wp option update home http://example.dev on the vagrant box current/ directory.
It’s strange that both siteurl and home are set to /wp. It could be that since wp gets auto installed, the settings for home somehow switched to siteurl one. I couldn’t find a way to set home programatically so it may be on some stage be put to the DB and loaded from there.
I also noticed that wp/wp-admin is used by the main site dashboard, but the network admin is loading directly from /wp-admin.