Is it because the atmosphere is much larger, and an optimal Goddard solution is achieved higher in the atmosphere?
It is no longer generally considered optimal to use a launch TWR of 1.5-3 in KSP. A little background: In KSP players who were optimizing for launcher weight would go for a TWR of 2.0 or higher, so players wishing bragging rights of "I launched 100t into orbit for only X tonnes of rocket" would go for a TWR of about 2.0 or even higher and this worked because a high TWR is extremely effective at mitigating gravity drag, a rocket with a TWR of 1.25 loses 80% of its thrust to gravity, while a rocket with a TWR of 2.0 loses only 50% of its thrust to gravity, a much greater fraction of the thrust is thus available for building velocity rather than fighting gravity and that makes the rocket significantly more efficient in terms of weight.
But as KSP development continued, career mode was released and the cost of rocket parts was balanced. At this time cost per tonne to orbit became a new and more legitimate metric for judging rocket performance. In KSP when you want to build a rocket which launches payload as cheaply as possible, often a launch TWR of around 1.25-1.3 is exactly what you want to use - at least for rockets which aren't using SRBs.
Now, why is this the optimal TWR for making cost-effective rockets both in KSP and IRL? What it comes down to is rocket engines are expensive but fuel and tankage is cheap, relatively speaking. Thus it is desirable to pile almost as much fuel onto the engine as it can lift to get maximum burn time out of the engine.
If in real life, there was some incentive to make launch vehicles which were as light as possible rather than as cheap as possible they would also have a higher TWR.
There are also other considerations that real spacecraft need to deal with, like gee loading. An initially high TWR will mean that your TWR at MECO will be even higher, potentially causing payload damage. Also, a lower TWR means MaxQ will be at a lower pressure. In real life, engine burn times are also much longer (usually) than in KSP, and generally that relates to a lower initial TWR.
No one mentioned aerodynamic drag. The faster the rocket goes in the atmosphere the more aerodynamic drag force.