The Exlorator comes with a default "boltgun", but as it is described in the book, it is a smaller (or normal-human adapted) version of the regular bolter that the Adeptus Astartes use (which is called Locke pattern). I would like to know, how different are these weapons? Is a "bolter" the same thing as a "boltgun"? If the Astartes bolter has .75 caliber, what's the smaller (?) version's caliber?
I don't know the exact rulings of Rogue-Trader, but I do have the Deathwatch manual on hand so can speak about some of the differences between Astartes and non- boltguns as defined in that manual, which (to my knowledge) is supposed to be compatible with Rogue Trader.
Firstly, boltgun and bolter are the same thing: they fire "mass-reactive shells called bolts" (Deathwatch Core Rulebook P146). There's no mention of smaller-calibre ammunition for non-Astartes bolters, only that "most bolter models have their roots with the Space Marines, despite smaller, inferior adaptations treasured by Imperial officers and nobles" (same page). Astartes weapons also count as "one Class heavier to anyone lacking in Space Marine physiology", and "impose a -30 penalty to all Tests made with them by presumptuous mortals due to improper scale, weight, and/or recoil--even in power armour" (same page).
The section on ammunition in the Deathwatch Core Manual (P158) takes care to explain that "bullets from one firearm cannot be used in another unless they are similar in make. Autoguns and autopistols can usually interchange rounds, but they calibrated bullets fired in terrible volleys from Astartes assault cannons are unique to that weapon." There's no such warning for bolt shells however! Everything points to .75 calibre bolt shells being the default for a "standard bolt weapon", i.e. both Astartes bolters and shoddier bolters.
Aside from the bits cited in ioanwigmore's answer, Deathwatch also assigns a higher damage value to Astartes bolters than to those made for normal humans. (Originally 2d10+5, later errataed to 1d10+9.) Since they both fire .75 caliber rounds, this implies that the Astartes bolters fire rounds which are either faster, denser, carry a larger explosive charge, or some combination of these three factors.
If the Astartes rounds have a higher muzzle velocity or higher mass at the same muzzle velocity, this would increase the weapon's recoil, explaining the increased difficulty for mere mortals to handle an Astartes bolter. It would also increase stresses on the weapon itself, making it dangerous (or impossible, if the cartridge is lengthened to allow for additional propellant) to use Astartes ammunition in a non-Astartes weapon.
Of course, that's all conjecture, given that this doesn't appear to have been directly addressed in canon.