How to change my logo size
Basically the logo gets the size of the uploaded image. If you activate the retina option, it will have half of the original size. For example you uploaded a logo with 200x100px. The retina logo will have 100x50px,
BUT, if you set for example the logo in a column that is smaller than any of the sizes above, the logo will be resized to fit the container. If you uploaded a big enough logo, just try to make the column where the logo is placed a bit bigger. For example, if the logo (with or without the retina option activated) has 100px and the column (container) has 70px, the logo will also be resized to the container size, just to make sure we avoid overlapping.
That should help you understand how things work. For some themes with predefined logos, some of the sizes might be hardcoded into the theme styles so that the header looks good on all devices.