This is largely untrue. MS-DOS and PC DOS were both built out of the same codebase for most of the time MS-DOS was on the market. They didn't diverge until some

This is largely untrue. MS-DOS and PC DOS were both built out of the same codebase for most of the time MS-DOS was on the market. They didn't diverge until some point after DOS 5 (1991). If you look at the MS-DOS source code, you'll see an IBMVER define that controls whether to build IBM PC DOS or generic MS-DOS. The option was there in the first place because Microsoft initially sold MS-DOS to OEMs as a generic 8086 operating system. In the early 80s there were a bunch of computers that ran MS-DOS, but weren't PC compatible. These largely died out as time went on. DOS was barely an operating system, so there were a lot of programs that bypassed it and accessed the hardware directly. None of those programs worked on non-PC clone MS-DOS computers, so most consumers chose PC clones for the far greater software library. What is true is that unlike most early 80s OEMs, Compaq built their version of MS-DOS with IBMVER set, so Compaq DOS was closer to PC DOS than many other early DOSs. As time went on and Microsoft started selling more and more copies of MS-DOS to manufacturers making PC clones, MS-DOS and PC DOS grew closer together, not further apart. MS-DOS 3.2 (1986) was the first version that Microsoft made available in a packaged form to OEMs that were shipping PC clones (it was still available as source code to OEMs who wanted more customization). For previous versions, OEMs were required to write their own versions of several hardware specific utilities (such as FDISK.COM and MODE.COM) that were originally written by IBM. MS-DOS 3.2 contained Microsoft-written clones of these utilities. MS-DOS 3.3 (1987) was written entirely by IBM (not Compaq!), as most of the key members of the MS-DOS team were busy working on OS/2. Because it came out after the Microsoft-IBM joint development agreement, Microsoft gained the rights to the IBM-written utilities and the packaged versions of MS-DOS 3.3 and all later versions shipped with the same utilities as their PC DOS counterparts. The closest thing to the claims this article makes is that Compaq did in fact maintain their source code license to MS-DOS and made enhancements to their version. The most notable example of this is that Compaq DOS 3.31 introduced a modified version of FAT16 that supported partitions larger than 32MB. I assume Compaq licensed this functionality back to Microsoft, as there's versions of DOS 3.31 branded for other OEMs, and support for Compaq's modified FAT16 (known as FAT16B) was included in MS-DOS 4.0.