Yes, "it's the Inquisition" really is the reason!
Sure, farseers can ally together, but then again, Farseers have been known to ally with Imperials too. Equally, Imperial forces from different brances regularly work together.
Make no mistake, however, this
is not an alliance. An Inquisitor can simply requisition any forces in the Imperium under penalty of excruciating death, no matter their command, mission or objectives. In practice this may be problematic (the Adeptus Mechanicus and Astartes can both make things particularly difficult) but any and all forces can be requisitioned.
"Each Inquisitor is a peer of the Imperium, one of a finite elite who hold ultimate authority over Mankind. As such, an Inquisitor can recruit any military or civilian force in the pursuit of Imperial duties, from hive world security details through to entire Space Marine Chapter, Titan Legions and vessels of the Imperial Navy."
There really is a good "background" reason for the Inquisition and
only the Inquisition being allowed access to other Imperial armies. I countered this by only allowing the Inquisitor to draw on resources from one of these military branches at a time (most normally an Inquisitor will only have the contacts or available troops from one, so it isn't too much of a far-fetched restriction.)
The other factor is that some people just don't like the idea of an Inquisitorial army that doesn't have Space Marines or Guard as its backbone, this was intended to allow them to flesh their army out with guard and make the Inquisitorial units more rare.