Note that the Old Ones (40k) are the same as both the First Ancestral Race (Evangelion) and Protoculture (Robotech/Macross) in this AU.

Faced with near extinction at the hands of the Necrons, the Old Ones designed "moon" carriers in which they sealed their souls. Spreading these "moons" across the milky way as seeds of life, they hoped to circumvent their fate. Two such "moons" arrived on earth (An event known as 'first impact'). Coincidentally, one had been corrupted by the chaotic forces of the immaterium during the journey, and its offspring possessed unnatural abilities enhanced by the warp.
Seeking to reverse engineer the Old Ones' technology, a secret organization inadvertently sets off' second impact', a near-apocalyptic explosion devastating the globe and sending the world into chaos. Global war is quickly ended in the wake of another development; around the time of 'second impact,' a giant spaceship of alien nature crashlands on earth. 'Second impact' is public blamed on the vessel's arrival and further investigation alerts humanity to an alien threat. The valentine treaty is signed, and all global wars end.

Earth's military forces develop what they call "Robotechnology"; transforming machines that convert into humanoid robots the predicted size of the aliens who owned the crashed spaceship. Now rebuilt, the ship is dubbed the SDF-1 (Super Dimension Fortress). Looking for the lost vessel, the Zentradi arrive and make first contact with humanity. Space war 1 begins.

During the development of Robotechnology, a top-secret project is developed harnessing the powers of the immaterium. These specialized conduits for the warp are named "Evangelions" and use DNA drawn from both the chaos corrupted and pure 'moons.' The secret organization conducting these experiments discover minor evidence for humanities' ability to control these powers but require the "EVAs" to enhance their strength.
Not fully understanding the SDF's capabilities, a small military force initiates a short warp-jump through the immaterium and arrives in Pluto's orbit. Their attention entirely focused on regaining ownership of the vessel; the Zentradi leave earth before the first 'angel' manifests. These angels are enormous chaos spawn birthed from the corrupted moon. Left to terrorize the world for several months, the angels force the secret organization to reveal project Evangelion to the public and temporarily postpone their goal of returning humanity to the souls the Old Ones left behind.

All angels are successfully defeated during the SDF's absence, but a massive Zentradi fleet arrives above the earth and begins an orbital bombardment. The destruction ravages 70% of the earth's surface and destroys all records and data on the Evangelion project. The secret organization is left in shambles, and their plans never come to fruition. The SDF's return marks the defeat of the Zentradi and their assimilation into human culture. Also spawn of an Old One's moon, the Zentradi are genetically indistinguishable from humans, and miniaturized Zentradi blend into human culture so well that later generations nearly completely forget their 'alien' heritage.
As per the Robotech trilogy, two more 'space wars' occur involving several different alien races. After the second, colonies are planted on mars. After the third, humanity sees a great time of peace and development. Using their limited understanding of warp technology, humanity can make short 30 light-year jumps as they begin expanding across the stars.

The peace is short-lived, though. The single empire of mankind begins to split and fracture as colonies are planted outside of earth's reach. The story continues along the path of the Battletech timeline until the 3,000s. Robotechnology develops into the LAMs of Battletech, and the development of 10-20m tall robots continues. Pilots of these machines begin to used battlemech neuro helmets which are crude wireless syncing devices between man and machine. This is in comparison to the Mechanicus' later use of hard-plugged princeps, as the wired connections prove more reliable in combat. Aside from the history put forth in Battletech, there are 14,000 years unaccounted for between now and the Dark Age of Technology in 40k. All knowledge of psykers is lost during this time, and the once encountered aliens have since gone extinct due to the decline of their own civilizations. Humanity thinks itself alone in the universe.

I put forth that due to the scale of Adeptus Titanicus, Battletech units and models from the Robotech RPG can be made to fight (albeit they are woefully underequipped) the knights and Titans of the 40k universe. Stat-wise, none have ion shields (so no saves!), but I would equate a large laser from Battletech to the Lascannon of 40k. Similarly, I would compare a Lascannon to that of Robotech's typical laser cannon.

Additionally, with the addition of a base commonly used by the reaver or warhound, one can convert the Real Grade Evangelion kits into scale miniatures. They stand 60m tall at scale, which just so happens to be the average of their purported cannon height of 40-80m. For these units, Ion shields would be replaced by AT-fields, machine spirits by the potential to go 'berserk,' and their ballistic weapons would be the rough equivalent of a Vulcan Megabolter.

For scenarios, I imagine a warp storm spawned from an attempted 'third impact' pulling mecha from their respective timelines and spitting them out in the 41st Millenium, as the immaterium has shown the capabilities of time travel to some extent. The Evangelion units would immediately be labeled as chaos engines due to their origins. The Zentradi of Macross would be quick to attack anyway. And it might just be fun to see Battletech mechs get stomped.