So how and when are you inserting the activity in buddypress?

Instead of applying a filter, you could directly publish an activity to buddypress using this trick. Wouldn't be that easier?

You could fire the save_post hook by your own may be, don't know if that'll work.

function wpufe_bp_activity( $post_id ) {
    do_action( 'save_post', $post_id );
}

add_action( 'wpuf_add_post_after_insert', 'wpufe_bp_activity' );

Then I suggest insert an activity manually. save_post only fires in wp-admin area. Implementing that hook in WPUF will create much trouble, thats why there are hooks given by WPUF.

Finally I gave a try to see what are you doing wrong. Turns out, bp_blogs_activity_new_post_content filter actually runs, but before any custom fields added to that post. So you can't get any custom field because no custom fields are there yet. So all you've to do is to update the activity with your desired content.

Here's how:

function wpufe_modify_bp_activity( $post_id ) {
    global $wpdb, $user_ID;

    //get the last inserted activity
    $activity = $wpdb->get_row( "SELECT * FROM {$wpdb->prefix}bp_activity WHERE secondary_item_id = $post_id AND user_id = $user_ID");

    // if activity found, update the activity with custom field
    if ( $activity ) {
        $content = $activity->content . '... Custom Field: ' . get_post_meta( $post_id, 'custom_field', true );

        $wpdb->update(
            $wpdb->prefix . 'bp_activity',
            array( 'content' => $content ),
            array( 'id' => $activity->id )
        );
    }
}

add_action( 'wpuf_add_post_after_insert', 'wpufe_modify_bp_activity' );

Adding the solution to the plugin core is a bad idea. Everyone doesn't run buddypress, so it's waste of 2 SQL query.