Is it me or are lasers breaking physics?

That laser won't do much, you'll be hitting the size of a coin, pretty much impossible to hit the same spot consistently and break through the armor.

That turret weighs over 300 tons and only has a 45 degree arc. That tells me the aperture is huge, which means a really tiny spot size.

So it's not breaking physics, the displayed number is a density, not a power total. You're delivering about 1MW to a roughly 0.0005m^2 circle. If you expanded that circle to 1m^2 at the same density you'd need 2GW, but you're not doing that so you don't.

hmm, looks like the laws of physics have changed yet again

MW/m^2 is a measurement like PSI. If I have a tiny 1/4x1/4 inch surface with 1000 PSI being applied to it, there's not 1000 lb of force being applied to the surface, but instead 62.5 lbs of force.

your example is backwards.  It should be that if you have a 1/4x1/4 inch surface with a 1000lb weight resting on it, then that area experiences 16,129 PSI of pressure.  This matches with our laser scenario of "X MW focused onto Y area yields Z MW/SI"

Area and diameter are related, but not identical.  A 3cm diameter results in an area of about 0.0007m^2 (which is still 7cm^2, because the conversion between m^2 and cm^2 is also squared).  So as you can see, the example numbers are a very close approximation.

Laser damage is (mostly) a function of energy density rather than total energy, because technically you're delivering a tiny bit of energy to each individual molecule on the surface (although the game doesn't model that level of detail, it can use some fancy math to approximate it) in an attempt to vaporize it. Higher density means each molecule hit will receive more energy even if less total energy is delivered.  It just means the molecules you're hitting will get vaporized with extreme prejudice, but their neighbors will be more or less fine.  Good for drilling tiny holes.  Or cutting things in half, since a cut can be made by a series of overlapping tiny holes that happen to go all the way through the ship.

Spread the same energy over a large area, and the low density means you'll gently warm the surface while the ship uses all that surface area to radiate the heat away.

Different materials can react in different ways though: a metal hit with a tight cutting beam might suffer from spalling due to part of it being flash-boiled, the resulting debris would punch large holes in the armor layers below it.  But that same metal, if being gently warmed by a wide-beam, would conduct and radiate the heat away without ever starting to melt.  A strong insulating fiber like silica aerogel on the other hand, might only vaporize a tiny pocket of itself and prove surprisingly resistant due to the vapor carrying heat away for it.  However, because aerogel has a low melting point and can't conduct built-up heat away, it can be easily "scrubbed" by having its surface gently warmed by a wide beam.

So in general, metals are vulnerable to tight beams and highly resistant to wide beams, fibers/gels are slightly/moderately resistant to tight beams and vulnerable to wide beams.  Against a combination of both, a tight beam will generally be better overall since fiber or gel can only delay it, not stop it.