I would ask a pharmacist, not a doctor, when you have drug questions, but I may be biased.

Estrogen can actually cause a decrease in the effectiveness of the thyroid hormone by increasing the level of thyroxine-binding globulin, and decreasing the amount of free T4. However, taking the pills a few hours apart is not going to change that. So I think the pharmacist was aware of the interaction, but didn't realize that changing the timing of the drugs doesn't really make a difference. It usually amounts to women on estrogen hormone pills need to have their levels monitored and adjusted accordingly if a problem exists.

But I'm not an RPh, just a PhD so I would talk to another pharmacist or ask this one to explain exactly why he recommended that.