What’s the reason against separate conduit for utilities?

If such a conduit would connect two sections that the hatch is meant to isolate, you would have to make the conduit and everything running through it airtight, even under a catastrophic loss of air. If the conduit didn't seal as well as the hatch, which is meant to withstand hard vacuum on the other side of it, it would defeat the purpose of the hatch.

They just didn't have enough of reserved general purpose connections for future use. I guess this woild be especially the case with the Russian modules, which were literally surplus Soviet manned space army outposts(such a thing do not make a lot of sense, they did it anyway).

Those would need to be connected during docking and sealed separately anyway if you wanted to seal the hatch. More failure points.

Just a guess: Harder to build and operate with more failure modes and less opportunity for intervention.

You'd still need to pull out the utilities and close a now second hatch in the conduit to seal the thing. What would be the point?