We looked into it and can confirm that PDF files flattened with PDFNet do not contain any information related to annotations of forms. The Preview is doing some monkey business to allow this sort of text editing. We tested this Preview 'feaure' on our end and found it to be buggy and unreliable.
There is technically nothing we (or you) can do to about this…. your clients can always temper with files (e.g. apply stamps, modify static content, etc.).
If you need to make sure that the original file is not modified, the right tool for the job would be to use electronic signatures (e.g. as shown in DigitalSignatures sample: http://www.pdftron.com/pdfnet/samplecode.html#Sig). With electronic signatures any modification to the file would invalidate the signature.
In case your main motivation is to enforce greater control over content (e.g. implement a custom DRM) you may want to take a look at WebViewer (http://www.pdftron.com/webviewer/index.html).