You specify include paths via the -L compiler flags.
I'm not sure what would be the best practices approach for doing this. You could add them on the compiler.*.flags properties or you could add them on build.extra_flags or similar. There is also the option of making the modifications in a platform.local.txt file (see I can not find the platform.local.txt documentation. · Issue #3371 · arduino/Arduino · GitHub). The main issue I would consider is that you want to make your modifications to platform.txt easy to port when you upgrade to a new version of the ESP32 core. I think the platform.local.txt would be the best way to do that because you would only need to remember to move that file out of the core folder before the upgrade so it wasn't lost and then move it back after the upgrade. I haven't messed with that feature much and as you can see from the issue it's not documented but with a bit of experimentation it should be easy enough to figure out.