Hmmm. You've got me curious now. The Beta website certainly makes it sound like a current practice. Check your shingle; according to the website, the charter would have the fraternity's Great Seal, but a shingle would have the chapter seal.
FWIW, here is the description from the Beta website:
The 1842 Convention authorized chapter seals consisting of clasped hands and the chapter letter to be used on the wax seals of letters. By the Civil War many chapters were using these seals and the use of an embossed seal consisting of the badge and chapter letter either above or below the badge became prevalent. The 1881 Convention re-adopted the original chapter seal concept specifying the addition of the three stars in a triangle surrounded by a circle containing the legend "FRATERNITY BETA THETA PI, 1839." Subsequently, the legend was modified to reflect the member's chapter. Today, the chief use of the chapter seal is on the shingle.
This is the example of the seal they show:
and here it is on a shingle:
I can tell you from personal experience that my uncle's Beta shingle had the chapter seal on it, just as pictured. A few years ago, on the fiftieth anniversary of his initiation (his "Fraternal Fifty"), he was sent a gold embossed Great Seal:
to place alongside the Chapter seal on his shingle. My impression was that this is part of the Fraternal Fifty recognition.