I'm incredibly small in my country because I live in the land of giants (the Netherlands is among the countries with the tallest people of the world). I'm sure I too have tiny hands and a tiny skull.
Like you, these were reasons for me to not transition for years. I would end up this tiny, odd looking dwarf freak. I did not want that. So I opted to try and live as female. Big mistake. Over the years I got more and more unhappy. Everyday there were reminders that my body was (seen as) female. It was horrible. So I gave in. I decided that I preferred to be this dwarf male freak than to stay a female. At least I was male then. I know that was a horrible way to look at it, and very disrespectful towards transman. But that was my train of thought back then.
Among cis men there is a lot of variation. Sure, on average they are taller, have bigger heads and hands etc. But there are also many deviations. You may think you have a small head, but there sure are cis guys who have that too. There is no rule. And it will not get you clocked. People may not notice and in the rare case they do they will think ' heh, that -guy- has a small head'. They will not think 'huh, that person has a small head so it must be female'.
Almost everybody has body image issues and would like to change some aspects. Of course, among transmen this is more prevalent, but also cis guys can be unhappy about a lot of things. They wish they were slimmer, more muscular, more manly, have a bigger penis, remove that ugly mole, you name it. Just accept that no one is perfect, including you. And focus on the things you can change instead of the few things that cannot change.
My story ends well. Once I decided to give zero ->-bleeped-<-s about my size and started to transition, a weight was lifted. Now, almost 2 years on hormones later, I'm very glad I finally made the decision to change my life. I'm seen as male all the time, regardless of the size of my body, hands and head. Best choice I ever made.