Hi Luke,
#1. Currently, Paypal or Google checkout are the only integration methods. If you have a coder, then it can be done. You just need to find out the post variables they require, modify the Market theme shopping cart code to prepare these variables, and then post to the URL specified for that gateway.
You may be able to gleen some more information from these posts:
http://www.markettheme.com/for…..the-system
http://www.markettheme.com/for…..ntegration
It is probably not possible to use WP e-commerce with Market Theme. Maybe with some customizing, but I'm not sure.
#2. The theme is very customizable. It has a bunch of built-in customization options, and then you can also edit the source code if you desire.
Using just the Market theme built-in functions, you could do most of the coloring, the logo upload, the thumbnail sizing, and quantity of thumbnails displayed.
Hope this helps.