Yep. It's like finding easter eggs, I guess. MIDI controller can be used the way you described also on Bassonist and the whole Sight Reading section, both competitions and training. I wish it was implemented all around the website, though...

How do I make my midi controller work with Notationist? Mine is not working.

@Amari Victoria : have you tried everywhere else (games I mentioned before) in ToneGym? If it works globally except for Notationist, then I have no idea how to fix that. But if you can't use at all within the website, you might go and check your browser's configuration on permissions to use certain hardware, etc. Otherwise I'd recommend opening a support ticket at Help Center where TG staff can help you for sure. Good luck!

and how do you insert the flats instead of sharps? (enharmonics)

Pressing and keeping down B4 + equivalent sharp note. Example: to insert Eb5, press B4 + D#5.

I could swear that one time, way in the past, I was able to use my MIDI controller. Something must have gotten set, somewhere along the line, as I'm not asked to use it (kind of like using the microphone, which it asked about every time).
I found this in the Help Center:
Can I connect my MIDI / How do I connect my MIDI?

Absolutely! Currently, the games that support MIDI connections are Melody Hunter, Notationist, Sight Reading Playground, Piano Recorder, and Interval Memorizer. To connect your MIDI, simply plug in your MIDI device to your computer. Once your MIDI device is connected, it should be automatically recognized by the system. If it's not, check to ensure the correct drivers are installed. Start your selected game and enjoy!

I had some problems with my old MIDI controller years ago, as ToneGym started implementing this feature progressively. If you add OS and browser constant updates, and hardware slowly getting obsolete (as my controller was during that period of time), anything can happen!

What I suggested was getting in touch with the support team via submitting a ticket (once you have checked FAQ section up and found no useful info, which you did). In the form you'll be asked to fill you can explain in detail what the problem is, and provide information about your controller, browser, computer... Staff will reply as soon as they are able, and they'll do their best to help and find a solution.