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You will find the following site helpful: http://technet.microsoft.com/en-us/library/cc721886.aspx The commands you are looking for are: bcdedit /delete bcdedit /timeout
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This has nothing to do with a new File System or windows moving to GPT partitioning. You can draw parallels between the dedicated System Partition on MBR disks created in Win7 and the ESP on GPT disks but this is created on disks initialized as MBR (NOT GPT). The main reason Microsoft created a dedicated System partition is to have a clean boot architecture for storage drivers that transform the OS partition and is required during booting. So, for something like bitlocker, this simplifies things since the bootmgr can come up in the regular way; load a simplified version of the bitlocker driver that facilitates booting the main OS and go ahead and load the encrypted OS volume. The same applied for VHD boot. If you already have an active partition from another OS (like Vista) no new partitions are created.
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The 200 MB partition is the "System Partition" required to boot windows and facilitates a clean way to activate advanced features like enabling encryption on your OS volume. Note that it is marked as the Active partition. When you start your machine, the stuff in the System Partition (like bootmgr, BCD store) gets loaded first (since the partition is marked Active). Next, the bootmgr loads up full fledged OSes (like XP, Vista or Win7) located in other larger OS partitions. This 2-phase approach allows Windows to quickly and easily load up the bootmgr without having to worry about advanced disk or volume functionality offered by drivers like BitLocker. In the second phase, the advanced functionality can be activated when the overall OS loads up. BTW, this 200 MB partition has nothing to do with the GPT protective partition. It is recommended that you don't use this partition to store other things. Hope this helps and clears things up.