In some point you are correct for the described behavior in other you could avoid it in some scenarios.
In case you need to update several control on separate manual ajaxRequest you could simple pass different arguments to the different requests, check this arguments on the server AjaxRequest event and proceed with the needed logic only in this case. Another option could be to use ajaxRequestWithTarget instead of just ajaxRequest.
Also in the example you mentioned note that due to the asp panels container nature, their content will always be updated no mater of the ajax initiator in once these panels are added as updated controls. In order to avoid this beahvior in the previous release we have developed a single property "UpdateInitiatorsPanelsOnly" which should be set to "true"
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