When I went to my first job interview, which was in person, I was a 190 lb woman who wore glasses. I've always had pretty low self esteem due to my looks, but I didn't once feel like they had any impact at all on the interviewers impressions of me.
Instead, I focused on things that did matter to the interviewers - an enthusiasm for the job and company, an interest in learning and a bit of confidence in my abilities. I think these are more important. Don't focus on what you look like! Instead focus on what positives you have to offer, like skills, a good attitude, and a passion for what you do!
I got that first job, and after a few months working there I came to the realisation that if you do good work and if you earn the respect of those you work with, you will be treated with respect and treated well no matter what you look like, (or what your gender is, in my case - I was in a male dominated environment too!).
As for skype vs phone call, video allows for nonverbal communication and I like to see facial expressions, etc, so I would pick video. However, if you wouldn't feel comfortable with video, then pick what will work for you. Ultimately, either will be fine and I doubt anyone is going to judge you on your choice. I don't think a video call will lessen your chances, because you're not being chosen for your looks.
Addressing the comments:
I don't deny that everyone will have inherent biases. However, It is a sign of a professional to put aside those biases and consider the important criteria instead. I expect this of the people I work with and I have encountered this the vast majority of the time I've been in the industry. It is a sign of maturity to look past the appearance of someone. As such, if someone is unable to do so then I will think twice about my willingness to work for them.