I'm not totally sure I understand your question. The originals are what are "stamped" and "penned" and they all have both types of numbers on them. Anyone who transcribes from the originals should tell you in the transcription which of the numbers they are using to index the image, but sometimes they don't (directly.) For example, here is the transcription for one of my ancestor's census records at FamilySearch.org:
Name: Cancel Cotton
Titles and Terms:
Event Type: Census
Event Date: 1860
Event Place: Election Precinct 11, Coffee, Alabama, United States
Gender: Male
Age: 7
Race: White
Race:
Occupation:
Birth Year (Estimated): 1853
Birthplace: Gea
Page: 189
Household ID: 1251
Affiliate Name: The U.S. National Archives and Records Administration (NARA)
Affiliate Publication Number: M653
Affiliate Film Number: 6
GS Film Number: 803006
Digital Folder Number: 005165577
Image Number: 00389
Household Role Sex Age Birthplace
Bradford Cotton M 60 Gea
Elizabeth Cotton F 40 Gea
Polly Cotton F 19 Gea
Jane Cotton F 16 Gea
George Cotton M 14 Gea
William Cotton M 11 Gea
Cancel Cotton M 7 Gea
The page number above is the "penned" number. The stamped number on the image, 937, is not mentioned in the index. I could possibly go to a different website and they could use the stamped number for indexing so with only the information above, if I couldn't find by name (in this case the name is misspelled so I might not find it by name) I would have a difficult time scrolling to find the image. So, it's important to know which of the two numbers a particular website or database is using for indexing.
Can you tell me where you read the article? If it's online, I'd like to read it, too, to see what they have to say about this issue.