When the description "just a PC" is applied to Steam Deck, it usually implies not just the x86/IBM-PC-descendant hardware configurations, but also the lack of strict software/hardware lockdown measures to prevent the use and execution of unapproved sw/hw. PS4/PS5/XB1/XSX are indeed similar to PCs hardware wise, but from this definition of "just a PC," they really aren't.
Optimizations on the consoles involve things like adjusting memory access patterns, using gpu-specific intrinsics and hardware specific latency info etc to tune the game engine. It's likely the same with Steam Deck.
There are a lot of generation specific optimizations that are often even exposed on PC but don't make it into any games because games don't often optimize for each specific generation of hardware (unless it's something particularly notable like DLSS/RT). This, I have noticed, is especially common on AMD recently, where some optimizations are very useful on consoles and eventually exposed on PC too, but never actually used there because of their issues until this latest generation.
Valve has probably worked to integrate those into Godot, there's also the consideration for power management, perhaps Valve has exposed additional APIs to make it easier for games to exchange information regarding power availability etc, so while most games just run as if they were running on a PC, there's the possibility for the game to also be Steam Deck aware/optimized.