What is Significance of MSR, SYS, EFI partitions for Win 8.1 Native Boot VHD? How?

What is Significance of MSR, SYS, EFI partitions for Win 8.1 Native Boot VHD? How?

I ask because I've built and native booted several variations of Win 8.1 VHDs on target SPro 3. I'd like to know pros & cons.

CONTEXT: 
So, with a lot of help and input from multiple amazing people from multiple forums and coming closer to the goal of my project. I have found and tested the ways and means to complete the steps in my project. 
Some interesting questions and thoughts have come up. 
(http://forums.mydigitallife.info/threads/62362-Virtualize-Win8-1-BIOS-MBR-Physical-Partition-gt-to-gt-WIM-Image-gt-to-gt-UEFI-GPT-VHD?p=1085352&viewfull=1#post1085352)

PROJECT MILESTONES SO FAR: 

A - Was able to find articles that help bypassing Sysprep errors on Win 8.1
Did some extensive Driver Cleaning/ Reseting from OEM/Intel/Non MS drivers to MS Win 8.1 native drivers

e.g. Prototype sample runs involved Sysprepping Fresh Win 8.1 installs while eliminating issue causing Metro App packages. 

B - Played with DISM, Disk2VHD, GPTGEN in various configurations with Win 8.1

e.g. Prototype sample runs involved imaging Fresh Win 8.1 MBR/ BIOS installs and converting or applying them to GPT/UEFI VHDs and native booting them in Step C

C - Have been able to Native boot Win 8.1 VHDs using BCDBOOT: 

QUESTIONS & DECISIONS about MSR, SYS, EFI Partitions on Win 8.1 Native Boot VHD: 

I am left with some final decisions to make and questions.. 

Before I apply my Customized_Windows.WIM...
What kind of Partitioning structure should I CREATE IN/ FOR my FINAL VHD? 

I ask because I've built and native booted several variations of Win 8.1 VHDs on target SPro 3. 
Some with Single Partition Volumes and others with Sys+EFI etc. 

OPTIONS/ EXAMPLES of Sample VHDs executed & installed on Surface Pro 3:

[:\Windows]
DISM Installed Natively 

[sys:300M][EFI:100M][:\Windows]
Vanilla Install via Hyper V
Possibly also doable using VDisk commands via Native Install as well. I guess. 
Also, during this Vanilla install it was trying to create the MSR partition in addition to the above. 

I did read about the MSR, SYS, EFI partitions online as well as how OSes can also run without those. 
https://technet.microsoft.com/en-us/library/dd799232(v=ws.10).aspx 

Also, if ever V2P for Upgrading to Win10 and then P2V again  There were some workarounds posted on Technet (need to find link, will find and post) as Windows cant upgrade on Native Boot VHD. 

BOOT BCDBOOT QUESTION: 
With single partition volume VHDs, its simple & clear how to APPLY and USE ..BCDBOOT. 
With these SPECIAL PARTITIONS, I am curious what would the best way to "direct" BCDBOOT > > > ?? From where to where? 
https://technet.microsoft.com/en-us/library/hh824874.aspx
https://technet.microsoft.com/en-us/library/gg577238.aspx

EXISTING HARDWARE PARTITION VOLUMES: 

SPro 3 HDD (UEFI Only):
[sys:350M][EFI:200M][:\Windows][Recovery:5GB]

X61T HDD (BIOS Only):
[:\Windows]