I have a little information for you, but not the whole answers, but I hope it helps some.

1. I do alot of work on computers, and I often see those small slices of extra space left over, some one please correct me if I am wrong, but I am pretty sure that it has to do with the type of partitioning that the Hdd recieved on how much is left over. I believe that is also has to do with the physical disk size and the formatted disk size as long as the file system clusters. I am not entirely sure, but this is what I believe.

2. Yes you can install more programs w/o doing a Hdd install, however you do need some type of media to store them on. You have multiple options of doing this. If you want to spend the time, and have the space, a remastering would be the best. If you don't, you can put a persistent home dir on an external device and use some programs that way. I know firefox and azureus don't need any other files that what is in their folders. (azureus does however need java). I believe that I also saw a discussion about being able to install other programs on external devices, that needed packages and the such, but I can't seem to find it right now.