From what I can see, You have to use a completely different method in order for windows to overwrite the MBR, so it shouldn't be able to do it through the system restore. Windows also shouldn't be allowed to alter partitions via that method either.
Although, if the last system restore state you have is before you partitioned, assuming you used Partition Magic or something, then I don't know what could happen. Windows will probably try to access data from the other partition if there was info on there before, as I doubt Windows will like the fact you altered something without its permission.
Which is why I format the HDD if i'm partitioning...