OP: Hopefully you'll be able to have relatively regular hours without having to file for FMLA. I would go that route first, and only file as a last resort. Maybe you'll have different schedules to choose from? Maybe some or many of your colleagues will be applying for schedules that wouldn't work for you, maybe they will even be paid more, but I would just request what works best for you.
BluViolet: I would never recommend disclosing your illness to your boss (or even co-workers, unless you're truly close); most people just don't get it and personally I don't expect them to. There's stigma, misunderstanding, as you say.
To be clear, in terms of the Intermittent LOA I've applied for, my medical information *only* goes to the LOA Coordinator at Occupational Health (in your work environment, it might be HR); that information is protected and my boss will *never* see it. I asked her to sign a form acknowledging that I'm applying for this under 'personal illness' with no other information. My doctor's forms will go to Occ Health, and she will never see them and they won't tell her. They will only tell her that I've been approved or not. If I'm approved, I assume they'll let her know that I potentially may need time off occasionally for my 'personal illness', without naming them, etc. So, again, I wouldn't reveal anything to your boss, or people at work; any application should go to HR/Occ Health and not be revealed beyond that. I hope this helps.
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