It would be convenient for citation purposes if the paragraph numbers in the published application match those in the specification as-filed. My suggestion is that, so long as the numbering in the as-filed specification meets the USPTO publication guidelines, the original paragraph numbering should be retained in the published specification.
The reason is that, while specification amendments are made to the as-filed specification, examiners typically use the published specification during examination. This results in potential ambiguity if the Publications Branch changes the numbering scheme.
In some cases, the original numbering scheme does not meet US publication standards, but frequently paragraph numbering becomes "a matter of design choice" by the Publications Branch.
This affects EFS web modernization because the published spec (in HTML) is part of the PAIR, SCORE and PALM databases.