Well thats basically what the global skybox cubemap (Now called Environment in Unity 2020) does.
Unity uses one global reflection probe that get baked for the environment (Unless you specify a cubemap that has already been generated) each time you build the export scene
So basically Unity does what you are doing. By putting an extra reflection probe in the middle of the scene and PRE-BAKING the cubemap, i think your just duplicating the global reflection probe.
By the way… All reflection probes (including the global unity environment cubemap) gets stored in the the scene folder that should be right next to the scene file itself.
They will be call ReflectionProbe-X… The last (or possibly the only) reflection probe texture is the global environment texture.
So if you only had the global environment reflection probe… It will be called RelfectionProbe-0.exr
if you create additional reflection probes… They will start at zero and the last reflecttion probe texture will be the global environment.
The exporter uses that global cubemap (Which is actually generated in the scene folder) via the RenderSettings.ambientProbe and set it the the scene.environmentTexture. This basically set that global environment texture for each PBR material in the scene (That does not have its own reflectionTexture).
But to answer your original question, if you want to manually create cubemaps of have more than the one global cubemap environment texture:
1… Create the additional reflection probes in Unity and pre bake the cubemap textures.
2… Manually add those reflection textures you just created to the scene export folder
3… In Babylon.js manually load the pre-filtered cubemap textures and manually assign them to what ever materials you want