OK... I said some time ago that my version started to freak out on the final level of Rowarty, so I am trying now the GOG version.

And I started to wonder - Say, is it actually possible that You can make the game crash on those final levels if You beat the previous scenarios via 'Mission Select' option while still playing the campaign?

It's like You completed South Dahshur scenario, but before moving to North Dashur, you first go to 'Mission Select' and play Buhen to beat it - This kind of gameplay.

Could that make the game freak out and make the final levels unbeatable?

No, it doesn't cause anything to happen. Any crashes that happen in game are due to reaching in-game limits (aka sprite limits in huge cities) or game engine bugs: the game will not "freak out" if you go back to other levels and play them separately.

And do You know, more or less, what are the sprite limits for this game?

No, I don't. All I know is that they're fairly high and can only be triggered in massive cities (anything over 15k has a chance to trigger the limit, though there are reports of people building well over 50k and still not triggering it)