Rather than trying to be all about the boogeyman, let's just look at the situation.
DQXI will most certainly help the PS4 and help it reach a better base for its other incoming titles to sell to, and DQXI will likely be the PS4s top selling release this gen (and may or may not outsell MK8, depending on marketing and release date... as I don't see DQXI getting a near 50% attach ratio on the PS4). This was no doubt part of SEs goal as they try to grow one base while serving another, and opening up western possibilities. However, we have to consider what has changed from when we had thought this was a PS3/PS4 title to now where it is actually a PS4/3DS title with differences in presentation but identical story structure.
The former, the PS3/PS4, would have helped the PS4 considerably more with a proper push because (a.) the PS3 has a decaying active consumer base, (b.) the PS4 is a natural upgrade path, and (c.) the enormous handheld base wasn't given an easy-out. So it would have been a good way to usher forward PS3 users into the PS4 and also snare handheld users with a must-have franchise. But, now that that isn't the case, we're actually looking at a scenario that will more closely resemble Smash and what happened with it. For whatever bells and whistles you might attach to one version over the other, the majority of the base is content with just playing the handheld version which better suits their lifestyle/gaming preference and also is content with not spending 30-40,000 Yen on another console for a game they already have access to and, for the most part, will get the same experience and story regardless. (However, on this point, read further down about what the DQH split also tells us, so its not quite clear cut how good/bad this move is for the PS4 at the end of the day.)
SE was in no position to put the title solely on the Playstation ecosystem it would seem, which largely seems to be about engine availability and limitations therein, as UE4 cannot run on PS3 or Vita, and they likely do not want to use or build any engine that can do it for all those platforms... so Phyre. In stead they elected, to serve a safe and large audience, to put it on the 3DS as well with version that, while not graphically capable, may actually end up being the more unique offering which... will entirely now come down to subjective views and nostalgia hooks. The 3DS version also demands considerable investment (aside from reusing assets) since it needs a dedicated engine and toolset for its games. I would not be surprised if we found out that Nintendo helped on the backend of making the development process for the 3DS version easier with engine tools already made for Smash/MH to truly push the system.
In the scenario of DQH, the PS4 version was 100% better in all ways, that is now no longer the case as unique features have been introduced. The DQH PS4 title also had a bundle to push it and heavy marketing targeting it. To some degree this shows that the consumer base will avoid adoption irregardless of the marketing and settle for what they have. And this was in a scenario where one version is objectively superior. If they had elected for a PS3/PS4 DQXI, we may have seen a similar scenario from the PS3 base. Its also highly possible that the successes of DQH were not what had been expected/hoped for, and that the 3DS version came into play later as the PS4 just couldn't gather the steam needed to justify a Playstation-only title. This is hard to say.
Given the above, I think that with the current release plans, we will see the last remnants of the active PS3 base/the Playstation old-gen base upgrading to the PS4 (I question how many will even be left by the time DQXI comes out) without given them an easy out. But, the change in platform expectations has given the handheld active consumer base (which is much larger than the PS3's active base) a reason to not need to buy a console at all. This leads to the Smash 3DS/WiiU split scenario where any real cross-over or double-dipping will be minor and the majority of the sales in either case will be to owners of the systems already.
So, as I said before, I think this will be a Smash-like split with a couple of caveats that may change things for better or worse ratios: when is the NX coming and out and when is the game launching? What version is the NX getting? Will the release really be simultaneous?