Thing is, I cannot believe that Apple supplied a machine such as fabulous as that with such an awful storage drive. Spinning platters, really? You can't tell me you couldn't have put a 128 or 250GB with a massive spinner for storage?
They supplied it with whatever you configured, including lame spinning drives or huge SSDs (for the time).
Furthermore, why haven't we made a software that makes it looks like you have both the boot drive and a storage drive appear as one drive but, make software store files only on the hard drive? (...)
How do you propose the "software" knows where to write each file?
You need to tell it case by case anyway, which defeats the purpose of having extra software in the middle.
You can already assign specific stuff to specific drives at the OS level (relocate Program Files or Users directory) or application level (like your Steam library / specific games to specific drives and so on). It's far more robust compared to some middleware or 3rd party API which intercepts your write calls (making them slow) and "guessing" where the file should go physically.
Besides, the window for "solving" this "problem" is rapidly closing as SSDs are getting big enough and cheap enough that applications are no longer needed to be installed on auxiliary spinning drives.