i don't think it affects your transition in anyway. shoes are shoes, and heels are heels. they're just footwear preferences.
if they're uncomfy, you don't have to wear them. i'm speaking on my previous experience before my transition along with my own experiences working in the fashion industry.
our bodies vary from individuals to individuals, some of us are very lucky with the body fat distribution a little bit different. it makes it so much easier slide in some heels and walk around in them. i don't say it'll be comfortable though. most heels are nowhere near comfy, especially the pointy toe/open toe ones. i find pumps are not bad actually, they have tons of varieties you can choose from. the higher the front of your feet is, the better. because it won't make your feet look like you're on some ballet performance for hours. if the weather is cold, try some chelsea ankle boots.
though, if you really want to start breaking in some heels and like to wear them often, it'll take some time getting used to. first five times were horrible i remember ;/ and whatever you do, invest in some good material shoes. so your feet will have some cushion and the pain is less.