Is there a standard Drupal way to link to 3rd party configuration forms?
For instance is there a Drupal function that takes the menu path (eg.
  'admin/config/system/cron') and provides an actual URL?


Definitely!

print l(t('Cron configuration'), 'admin/config/system/cron');


Will print an a tag as follows: 

&lt;a href="/admin/config/system/cron"&gt;Cron configuration&lt;/a&gt;


to the configuration with paths resolved correctly (works well when you have installed Drupal in a sub folder as well - just use the Drupal path). 

If you are putting your own text, most likely that you are using t() function. 
Example: 

$form['warning']['#makup'] = t('You need to make sure that you have setup a working !cron',
  array('!cron' =&gt; l(t('Cron configuration'), 'admin/config/system/cron')));


l()  -  Generates the anchor link (&lt;a href="path/to/page"&gt;text&lt;/a&gt;)

url() -  Returns URL for a given Drupal path (l() calls this function to get the correct link)

See function reference for more configuration (absolute URLs, prevent using aliased path, etc)