I'm on intermittent FMLA and I am also in HR. I have only once worked for a company who had someone else handle their FMLA. It was a huge company. My current employer is pretty large, but the HR department handles it there. I have been on intermittent FMLA continuously for about 2 1/2 years and have never had any problems with them questioning anything. The dr. says that the frequency and length of the flares are unknown/not predictable and that has always been sufficient. Just have the dr. say as much as possible (i.e. "flare could last 2 weeks to 2 years" or "last flare was 6 years"). Hopefully they will get the idea then that it's not something he can put an exact number on.
In working in HR at several companies, I've seen some that believed every single person was abusing FMLA (except for pregnancies...everyone is all happy if you have a baby, but not sympathetic if you are ill) and some that are great about it unless they suspect you are abusing it. And people do abuse it and it makes it more difficult for people like us. People at my husband's work actually call it the "Friday, Monday Leave Act" because so many people abuse it and only call in on Fridays and Mondays. That's really sad when many of us have to jump through hoops to get it approved.
I had one manager at a previous job decide I was abusing it because the doctor told me to do pilates or walk to help relieve stress (when I wasn't eating and my heart rate was 200). Since I was able to do that on occasion, she decided I was abusing the FMLA. At my current job, my boss's daughter also has Crohn's, so she completely understands. It all depends on the company, the HR people, their policies and your boss as to how easy they will make it be for you to qualify. That's the sad truth.