If we are talking about workaround for additional directives I could recommend you use after migration hooks to copy missing configs. From Plesk`s side, additional directives placed into file vhost.conf which included by httpd.conf. The trick is to copy vhost.conf from source and run /usr/local/psa/admin/bin/httpdmng --reconfigure-domain <subscription>, as result httpd.conf on domain will include vhost.conf.
So, first, prepare script to copy vhost.conf(vhost_nginx.conf for nginx) into /var/www/vhosts/system/<host>/conf/ and to run /usr/local/psa/admin/bin/httpdmng --reconfigure-domain <domain_name>, the second, add after migration hook:
1. Create directory for scripts, if it does not exist yet:
mkdir -p /usr/local/psa/var/modules/panel-migrator/events/subscription-migration-finished/
2. Put prepared script to created directory and make it executable
Unfortunately, only subscription name could be processed automatically by getting first command line argument, for example:
#!/bin/sh
echo `date` $1 >> /root/finished
So, if you have a lot of subscriptions and minimal number of addons - use this workaround.
If there are a lot of addons, copy vhost.conf files manually and run /usr/local/psa/admin/bin/httpdmng --reconfigure-all
If we`re talking about data from nginx settings and Common Apache settings sections, all should be migrated without any workarounds and if it doesn`t so - let us know, we will continue investigations.