This has been my experience, also. Due to some very terrible sleep problems related to my fibromyalgia, my dosing schedule was all over the place at one point. It actually got so bad that I had to cut my metformin dose in half because I'd end up taking my pills too close together and having gastric issues from those also.
Getting up, taking a pill, and then waiting 30-45 minutes before eating just wasn't particularly doable for me due to my Dawn Phenomenon anyway. My blood sugar starts rising the minute I get out of bed and could easily go up 30-50 points during that time - or at least not come down at all, even with a small bolus, if I don't eat.
The solution has been for me to take my Levothyroxine at night, right along with all my other meds. I take it at a consistent time, in a consistent way, at the same time I take my basal insulin shot. My doctor simply adjusted the dose accordingly. Am I taking a slightly higher dose than I might otherwise be? Possibly - but the dose I'm on costs me the same as a lower dose would, and my body's clearly only going to absorb a certain amount under the circumstances its taken in. And it means a great deal more convenience, less insulin to cover my DP, and peace of mind for me.