That’s the power of open source! 
But of course when you do that you are on your own and it may become harder for you to get support from us. But you know that already. We do recommend disabling and creating new flags instead of changing them via the console, once they have been used.
This is just a hidden setting and can be increased. Folks on our hosting that are bumping up against that limit can reach out to us to increase it for them. It will also be interesting for us to hear from customers about how they are using the custom flags and why they might be needing to make so many changes!