Let's try this one last time. Step by step, using this check as an example:
1. The check is written.
2. The revenue stamp is applied somewhere on the document.
3. The stamp is canceled by the business in ink with a pen or handstamp of some sort.
4. The amount of the check is embossed with a "check protector" similar to this one currently running on eBay
5. The check is transferred (handed, mailed, who knows) to the recipient and is processed through normal banking channels. Done.
In your case:
6. Somehow the stamp got the security embossing on it too. Nothing more. An accident or on purpose, who knows. Without the full document and the clerk's mindset there is no way to precisely know. Does it really matter?
7. One small difference, as noted in my first post, your stamp was likely on a promissory note (rather than a check), which does have superficial similarity to a check but is to be paid at a later date and is taxed at a different rate, thus the higher denomination. The steps of its creation are the same.
8. It will help your understanding if you can separate in your mind the use of postage stamps and revenue stamps. Your stamp has nothing to do with the 1870 era grills on postage stamps. It has nothing to do with envelopes or going through the mail.