You get the form entity using the form_get_maps(form_id).
For each entry in the maps, get the field id for this entry
This field has an internal_name, which if matches, should be set with the form

I'll see if I can use flexprofile_set_data() function instead. Will report back results.

form_set_data($entity, $data)

This function takes an array data, with the internal_data strings as array access keys, which has instantiated stdClass() objects per field definition (internal_data strings). The attribute "value" stores the value respective to it's internal data string.

$entity is the ElggEntity that allows metadata, for flexprofile, it's the ElggUser.

Looks like form_set_data() and flexprofile_set_data() are exactly the same function.

Looks like the metadata is being set using create_metadata(), so you can technically get the $user object and just use the regular metadata methods to set and retrieve values.

For example, if a form field internal_id is "flex_plugin" then $user->flex_plugin = "somevalue"; or echo $user->flex_plugin; would work

Yep, just confirmed it

$user->setMetaData(%internal_name%, %value%);
$user->getMetaData(%internal_name%);

works fine.

I think it would be wise, however, to use form_set_data() to control the access. You can always use access_id to override it.

Hope this helps someone:)