Why would ammo compatibility be a problem in a setting where all production is governed by galaxy-spanning organizations? They could figure out unified lasgun charge packs, but can't figure out standardized cartridges? It doesn't hold up.
Which galaxy-spanning organisation is governing the production of some random underhive's gun shop or a sanctioned manufactorium as long as they are paying their fees? The rulebooks talk about a "galaxy of guns" and throw like a million local gun patterns at us. If individual planets have their own gun models, why shouldn't they have their own ammo specs as well?
The AdMech doesn't care as long as the manufacturer adheres to its religious mantra. If they are even aware of the maker.
I wouldn't even be so sure about unified lasgun charge packs - though I am of the opinion that they'd have a unified adapter, making sure they can all be plugged into the same generators and energy distribution nodes. The only projectile ammunition type that has ever been mentioned to be standardized is bolt shells, and those are described as being so hard to get anyways that it may just as well be the same here.
Basically, because to assume otherwise would attribute the Imperium with the level of idiocy that no amount of hidebound fanaticism begins to explain. It would require everyone in the Imperium to ignore the obvious benefits of having standardized ammo for no reason but... to be unique?
Note that the Imperium explicitly benefits from standardization in many other areas, thanks to all the scraps of the STC. Now, being able to load your gun is an important issue in a galaxy-spanning civilization that's obsessed with war:
If I'm a high-ranking commander of an IG regiment, I want my men to be able to share ammo with as many allied units as possible, because in a pinch, two shooters with one magazine each are better than one shooter with two magazines.
If I'm a Rogue Trader doing (often violent) business all over the sector, I want to be able to restock in every port I'm in.
If I'm a planetary governor responsible for arming the enforcers and the PDF, I want them to use unified equipment, because it makes logistics that much easier - and if at all possible, I want them compatible with whatever forces are most likely to come to the planet's aid in case of serious trouble, because it may be a matter of life and death for both my men and theirs (and consequently the whole planet).
If I'm a pilgrim buying a pistol to defend myself en route to the Shrine World, I will buy the one for which I will be able to buy ammo wherever I go.
Mind you, I'm not saying the Imperium has two or three types of bullets overall - I'm saying certain types of ammo will be vastly more popular, to the point of almost universal availability, and even some weapons with less common ammo might be built in a way that allows them to shoot more common ammo (like IRL Magnum revolvers can shoot non-Magnum rounds of same diameter).
Also, barring all that reasoning, telling players they can't reload their guns because local autoguns, despite being entirely identical to theirs in every comparable aspect, have a slightly different caliber, is a major **** move.
It's not a concern, until you need to spend more than a round reloading. Once the actual shooting starts, the reload time is more of a factor than the number of bullets you're carrying.
Hmmh this probably wouldn't apply to the heavy weapons with backpack supply, but I'd say they come with other issues.
It does make me wonder if perhaps the designers meant the autogun's ROF of 10 as a drawback rather than an advantage, though...
Well, it's certainly a drawback in BC and further. In previous systems, it's not actually inconceivable to make most of these rounds hit their mark. Not on an average starting character (except in DW, but this game is a different beast for many reasons), but overall quite possible.