Mm... re: XCOM in WH40k land, barring integration into the imperium from very early, they'd kinda' be shot for techno-heresy in like, five seconds flat.
In general, and how I've seen it treated in various fan works, XCOM's really scary bit isn't their displayed combat capability (As noted, they're only about on par with stormtroopers thus far -- minor genetic engineering or doping or... something with decent-ish kit and incredible training), but their
reverse engineering ability. Going from barely future/now past military tech to freaking plasma cannons, flying armor, and ufos in... what? Month or two? You've got a by-day thing going on there in game. That's frakking ridiculous.
XCOM is a snowball faction -- they start basically melting but within a few rolls they're using all your shit to shoot you back and they've probably improved half of it, turned your pet tribble into a war machine or something, and dissected your extraterrestrial livestock. Maybe just for fun. The Adeptus Mechanicus would flip their collective shit about three minutes after XCOM's scientists and engineers started doing their thing. That said... them and the Ordo Xenos would probably get along pretty swimmingly. XCOM's got xenophobia down pretty hard.
It's worth noting that XCOM meets <Whatever> has had some pretty decent fanfiction written for it, for several of the notable series.
XCOM vs. Starcraft is roughly the same thing as XCOM x WH40k (surprise surprise
). If they survived dealing with a zergling or whatever long enough, you'd see hybrid terran/protoss tech popping up within... months, probably, and Zerg physiology somehow being used to power doomcannons or something. And gods help everyone if they get their hands on Xel'naga tech. That's kinda' what XCOM does. They're actually pretty wanky in some ways.