How to change search_api_server options via CLI
This problem was probably specific to Drupal-VM, but here's how I solved it. Rather than write a post-provision script that tried to run the sql command itself, I made a new file containing the sql command and told the post-provision script to use that file.

So instead of the script running this itself

sudo mysql -u root -proot drupal -e "UPDATE search_api_server SET options = 'a:14:{s:9:"clean_ids";b:1;s:9:"site_hash";b:1;s:6:"scheme";s:4:"http";s:4:"host";s:9:"localhost";s:4:"port";s:4:"8983";s:4:"path";s:17:"/solr/collection1";s:9:"http_user";s:0:"";s:9:"http_pass";s:0:"";s:7:"excerpt";i:0;s:13:"retrieve_data";i:0;s:14:"highlight_data";i:0;s:17:"skip_schema_check";i:0;s:12:"solr_version";s:0:"";s:11:"http_method";s:4:"AUTO";}' WHERE id='1'";

It now does this

sudo mysql -u root -proot drupal &lt; $SEARCH_API_SERVER_SETUP_SQL_COMMAND_FILE

(Replace -u root -proot drupal with your sql username, password, and the site db)