This article is not very clear. After the author realizes that they don't have low-level access privileges they just... do the thing that failed 20 times before and suddenly it works with no explanation as to why.
It’s important to realize that Windows XP was the successor both to the NT line (Windows NT/2000) as well as to the DOS-based consumer-oriented line (Windows 95/98/ME), hence upgrading from Windows 98 to Windows XP is the natural path, whereas upgrading to Windows 2000 in between is kind of a detour.
I agree that the low-level explanation is lacking, but in fairness dosbox-x doesn't sound like it offers that (out of the box).
I'm guessing what happened, the boot sector etc. were installed by 98, win2k had some way of converting from FAT32 to NTFS, and the winxp installer just sets some flags and dumps install files on disk somewhere.
Getting all that from "it's the NT conversion" is a stretch, but.
Note that I was totally skipping the text-based installation stage when upgrading from Windows 2000 while I got it when starting the installation from Windows 98 - that's where the "NT conversion, stupid!"-theory came from.