This thought came to me after reading an old interview by Douglas Goodall on how the main quest of Morrowind was written. The gist was that, for the Red Moment, vanilla's devs had written up several different interpretations, and then never reconciled or even declared which one was the truth. All the interpretations then made it into the game, with different factions believing different stories. This served the purpose of the player being able to choose the truth, as well as lore fans theorizing that the Battle under Red Mountain was a Dragonbreak.
I'm thinking we could use this same tactic for TR's Hist-Dres problem, with some tweaking. It would be a nice little nod to the themes of TES3, but also helps us solve the problem of how to better define this in the Dres faction storyline.
See, we've got several pet theories running around for why Hist and Dres would want to ally. Among the ones I've heard (and sometimes they are combinations of these, or variations, so excuse any misrepresenting as this is more to make a point than flesh out each interpretation currently)...
--the Hist is implanting sleeper cells within the Dres ranks which will eventually culminate in an invasion
--the Hist send out Argonians to observe the world as passive scientists and scholars
--the Hist care little for the Argonians and they use both them and Dunmer in experiments to create new lifeforms
--the Hist barely even realize what they're doing, and the Dres councillors have just assumed they have gotten the go-ahead to take slaves
--the Dres councillors made their deals with rogue Argonian tribes due to the all-around vice of greed, and the Hist weren't truly involved
--the Hist tasked the Dres wise women of old with helping them to regulate their soul matter run-off, and the Dres wise women are thus actually Argonians (the religious soul-sharing kind, not the lizard race)
--the Hist have wars between themselves, and the Dres allied with one (faction) of them
--the Hist, being aliens, have completely incomprehensible motives and there's no point trying to figure it out
Instead of trying to narrow it down to just one or two of these, what if we did what vanilla's devs did, and write plausible legends for each one for use in TR? Perhaps each Dres councillor has a different story to tell to the player towards the end of the Dres questline, plus a few Argonian shaman sorts (are we going to use the Tree-Tender lore?) for players who are not part of House Dres. The differences in the accounts could be chalked up to madness/amnesia on part of the councillors, and the difficulty of deciphering spiritual mumbo-jumbo by the Argonian shamans.
Or, if we wanted to get even weirder, we might try delving into Dragonbreak territory. The Hist are apart from the world and not necessarily governed by the Earthbones laws. A few possibilities here...
 The Hist-Dres alliance happened inside a Dragonbreak. Maybe this was part of the Red Moment (I believe the Warp in the West is too recent?), or we could follow fan theory and put in a Dragonbreak right during ESO times. The latter would allow us to draw on the notion of the ESO Ebonheart Pact and the Argonian/Dunmer alliance there.
 The Hist are only incompletely affected by Dragonbreaks. Being outside of time, for them the effects of a Dragonbreak go on forever instead of just during that particular moment on Nirn. What this means in more meta terms is that, for the Hist, the retcons between games never happened. The inconsistencies between TES1, TES2, TES3, Redguard, Battlespire, TES4, TES5, ESO, ES:L etc etc do not exist for them. Therefore, all the above accounts of the Dres-Hist alliance are also true. The Hist do nothing because they are essentially paralyzed--they can't both attack their loyal allies and take revenge against the Dres, etc.
 The Hist are drawn to the Towers, but any time they get too close to them, their reality clashes with Nirn's and has fits that may mimic the effect of a Dragonbreak and other timey-wimey weirdness. (A similar effect to when a mortal drinks Hist Sap, perhaps?) This could serve as another reason for the Hist to ally with the Dres: the Dres maintain a buffer, as well as allow small bits of Hist (in the form of Argonians) to come closer to the Tower to cultivate an immunity/innoculation over time.