Penetration, faster swap and eventual ammo efficiency are great and all, but bolter can hose down a wide swath very quickly instead of relying on pen, projectile is hit scan with no charge time delay (even on plasma hip).
As for penetration, bolt has some trash pen and some door/floor pen (beyond explosive?) and whatever other magic mentioned in notes. Then there are the things the plasma can’t do: e.g.the bolter can clear little shooters much better, whether it’s picking them off or spraying a line of them crouched etc.
There’s a lot of overlap, but overall the bolter got buffed a lot outshines the mighty plasma, at least for now. It’s likely to get toned down once they fix the root cause of the aim/recoil/sway jank.