I wondered the same, and I would assume it's the same for me (MTF), as we're both replacing hormones. Thankfully, at no point during my transistion has my dog ever seemed confused, or treated me as a new person he's just met, and so far I've been full time for about 3 months.
I think as long as your pets see you everyday, they probably don't notice (or care) as long as they get their food and treats!