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There is no restriction where the Munchkin can be posted. It retains all native functionalities and interactions with campaigns.
The drawback of a distinct top-level domain is the fact cookies are domain-specific therefore known leads in one domain will remain anonymous in the other domain until they click a tracked link, merging the two records.
There is no user-niticeable delay when posted within a web application. An important consideration is the use or not of jQuery libraries on the application. Adopting the "Simple" Munchkin is a safer option if the application loads jQuery libraries. The Asynchronous and Asynchronous jQuery can be used provided jQuery noConflict is added to the Munchkin calls to mitigate versioning conflicts.
Drupal and Wordpress are good examples of Munchkin within applications. I know a customer running Munchkin to track actions within a geographical information system.