You can use the checkbox, but there is no reason for it to exist. I put it in before we (I) knew that you can synthesize any candy you have in inventory, regardless of your path. That flag also appears in the "flags" argument to the API, and should be removed everywhere.
It's been on my list to do for a long time, but it doesn't bother me persionally (since there is the easy workaround), so I haven't cleaned it up.