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I agree with the point on microtopography; the terrain in Rimworld is largely either flat or mountainous, with no rolling hills or anything like that. However, I think you are taking the analogy to WWI tanks a bit too far. I was using it as a way to describe how centipedes are
used, rather than how they compared to other units present during WWI. Also, you're kinda discounting the
heavy weapons that
those tanks used, which I feel contribute to the point I was making that centipedes are shock units. In other words, they're used as heavy shock/breakthrough vehicles that can punch holes in your defences that lancers and scythers can then exploit and must be addressed as such. The role they play is of units that must be treated with caution, rather than regular raiders or even lancers/scythers. The weapons that centipedes use are strong in comparison to the weapons that your colonists typically have, which, again, makes them highly suitable for being shock units. Explosives in general are just very difficult weapons to fight, so you must prepare for them. A centipede using an incendiary launcher and a regular pirate raider using a regular incendiary launcher will both shred a colonist to pieces; it's just harder to tackle the centipede.
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Centipedes don't fire their main weapon if caught in melee
before they begin aiming. If they are currently aiming at a colonist and you melee them, their behaviour is the same as that of all other pawns; that is, they will finish their current firing cycle before beginning melee combat. Never engage a heavy charge blaster centipede that is aiming at you in melee combat for that reason, as no amount of armour will prevent the centipede from eradicating a colonist's head or torso in one shot. By the word "bigger centipede", I assume you're using a mod, so I don't really have a baseline to go by in that case.
With regards to trenches, the advantage embrasures have over trenches would theoretically be that soldiers firing out of a bunker can fire over terrain such as rock chunks. In Rimworld, since everything (except said rock/steel slag chunks) is flat, trenches would work very well until/unless there is a rock chunk in the way. Since CE models cover as being of certain "heights" rather than vanilla Rimworld modelling cover as being of percentage effectiveness, I'd imagine that trenches would have to place pawns
below regular height, which means that pawns within trenches would be unable to fire over sandbags, chunks, and possibly fences if mods add those. I don't know if doing this is even possible, but in order for trenches to be differentiated from embrasures, this would, in my opinion, be the most logical way to treat them. Otherwise, trenches would be superior to embrasures since trenches would probably take no resources to build, only work time (you're just digging in the ground after all). There are already mods that provide trench digging, so I'd look into those if you're interested in digging trenches for your pawns.
With regards to ammunition damage, it's true; there is a certain strangeness to how all cartridge types behave the same way when used in different weapons. I think in general, since rifles typically do not fire pistol cartridges, and pistols do not fire rifle cartridges, it's okay. There are very few instances where two vastly different weapons share a calibre. Two off the top of my head are the M3 grease gun and the M1911, which both fire .45 ACP, but the difference in muzzle energy is not vastly different. You wouldn't be using a grease gun to penetrate armour plating over an M1911, after all. And if you're talking .22LR, well, that round is so weak that the difference in penetration wouldn't even matter. I think the range differentiation between pistols and rifles does an overall good job of modelling the differences in how these weapons would be used at this point in time. While I don't think it's absurd, I do think that it could be reworked a bit; it's just that the difference would barely impact anything for a fair bit of added complexity.