The schools have enrollment caps, so for the schools that follow their enrollement cap, the tuition deposit is their way of making sure you will be attending. It makes it harder to cancel at the last minute when you lose a significant amount of $. This is pretty common practice in pod/med/dent/grad/etc programs. Some competitive pod residency interviews, and even clerkship slots, do the same thing.
You cannot just "add that in to your loan." The entire point of the deposit is to get that money early as a gesture that shows the accepted student is committed to attending. If you have not paid your deposit, then once the school's annual enrollment cap is near, seats would be offered to other applicants, they are invited to put down their deposit, and you lose your spot if the class hits capacity before your deposit is paid.
At this early stage in the cycle, you don't really have to stress over the schools that pull that stupid "Congrats, you're accepted. You must send deposit within the next 2 weeks or you lose your acceptance." That is sometimes just a marketing game to get you to cancel interviews/visits to other schools. However, be aware that some programs will fill. It all varies from year to year, but I think Barry and one or two other pod schools were on a waitlist by March or April this past cycle (entering c/o 2012). Some pod programs that get less interest and/or accept larger class sizes) will accept students right up until the start of classes in Aug or Sept in order to collect more student tuition, though.
