This thing is odd, because most companies I've worked for have pretty strong bans on making statements like this outside of official channels.
That said, frankly its probably not a big deal because reactos, has been pretty clear about making a best case effort to avoid this kind of problem and solving it when it happens. Hiring 3rd party IP review companies to compare their code with the illegitimate windows drops is probably fairly inexpensive (given how much I seen paid during acquisitions I've been involved in) and something I imagine they have done. Its the kind of thing I might even expect that having a dialog with the right people at MS might go a long way to helping reactos avoid infringement. Heck it wouldn't surprise me if MS would fund something like this.
OTOH, it might take a more premium review service to assure compliance. I spent some time reverse engineering win2k, reading the native api book, and various other books full of windows reverse engineering documentation at the turn of the century for a driver project I was working on that hooked into some unusual parts of the OS.
NT has some wonderful documentation available which paints all the broad strokes, combined with Microsoft's own docs/samples/symbols/checked builds/etc and the fact that large parts of the OS seem to be written fairly well (and seemingly avoid a lot of spaghetti) doesn't lot of black box areas. NT also does a fine job with very verbose and descriptive variable and function names (unlike large parts of linux written to conform to 80 columns where frequently the solution to overrunning the column has been to name things very tersely).
So its not surprising that there are directory structure similarities. The natural thing to do is put subsystems in their own directories and nest them logically with the over arching architecture. Big swaths of the code are likely fairly similar as they fill out particular structures mostly with public field names, or even in the cases of non public fields the verbose NT naming convention would lend a reasonably high probability of name collisions in the undocumented parts.
Finally, if anything the two black binders full of internal secrets actually seem a bit weak. Looking at the long untouched part of my bookshelf with NT documentation, I have probably two feet of books not published by MS that are either entirely dedicated to reverse engineering, or are targeted towards driver writers looking to expand upon the official microsoft documentation. Including a black binder about half the size of the pictured one with various magazine articles, internet articles, etc I printed and bound during that two and a half years of my life.
Lastly, given I've spun up reactos a few times in a VM, I don't think MS has anything to worry about. I would love an opensource win2k clone, but its frankly no where near done. Some thing work really well, but many things simply don't work at all, or the thing crashes. Last time I ran it, the image ate itself. I'm also guessing more than 1/2 the work is being done by the wine project as they re-implement the userspace side of things, the core NT kernel simply wasn't that big in the win2k timeframe. If reactos had 1% of the developer effort that the linux kernel+core subsystems (systemd, dbus, etc) gets it would be a near perfect clone by now. After all MS wrote the thing in 5 years? (Cutler joined MS in '88, and NT 3.1 was released in '93).