Thanks for being patient. Our development team has completed the analysis of your issue (WORDSNET-8619) and has come to a conclusion that this issue and the undesired behaviour you're observing in Aspose.Words is actually not a bug. So, we will most likely close this issue as 'Not a Bug'.
The reason why hidden text is visible is that your document has display option to show hidden text. This is independent of "show control marks". You can access this option in Microsoft Word 2013 through File->Options->Display->Always show this formatting marks on the screen->Hidden text. There is also an explicit option "Print hidden text" right below under the "Printing options". So, the hidden text is displayed because of the view option set in Microsoft Word. This option is not part of the document. In order to make hidden text invisible again, please remove this option in Microsoft Word. Unfortunately, you can't currently control the behaviour of this option using Aspose.Words. We will expose this option in the public API in the coming releases.