You are correct – the script adds this non-existant folder to the include path. This is done here
In the previous 2.7.4 core version, this directory did exist. In the latatest 3.0.0 core version, it does not, but the Arduino-ESP8266 people did not update the platformio-build.py properly to reflect this change.
If it really bothers you, you can apply this change locally by modifying C:\Users\<user>\.platformio\packages\framework-arduinoespressif8266\tools\platformio-build.py with the changes shown in the PR.
However, this has 0 effect on any built firmware. Since these directories don’t exist, they are just ignored. This cannot cause a non-working firmware etc. It is just that VSCode complains (correctly) about being given a non-existant include directory.
Even if it gets accepted quickly in the Arduino-ESP8266 repository, it will not be used instantly by PlatformIO. It’ll just be there sitting in the master branch. PlatformIO only updates its internal Arduino core package when a new release comes out, see here.
This will then however be a per-project fix. And you will have a slight discrepency between the 3.0.0 release version of the core and the bleeding-edge git version of the repo, potentially causing bugs.
So, I’d rather advise to do the change once locally in platformio-build.py, this way it automically fixes it for every project using this core, without using special instructions. In the core version after 3.0.0, this will be fixed automatically then if the PR is accepted and PlatformIO updates to it.