@bgoel4132 first about /vendor partition handle. It is possible to use standard TWRP with my repartition scheme in this case /vendor will be just hidden and there would be no opportunity to interact with it through TWRP interface. If UA TWRP is installed + repartition is made and you get error with mounting it, then just format it via Advanced wipe menu. On stock partition layout UA TWRP will give continuous error with unable to mount /vendor.
About stock. NO ONE MUST NOT FLASH PURE STOCK it is super bad idea. Never do that. Instead there are 3 solutions of stock flashing problem:
1. Backup your stock rom with TWRP (boot+system) and then restore it after repartition.
2. Unpack pure stock image and flash ONLY system image through fastboot mode.
3. Flash stock rom repacked for flash via TWRP (I'm Nexus 5 owner so I don't know if there are such roms for mako).
P.S. And remember don't do anything if you aren't certain in your actions. Check thread or ask, it is better than have more problems in future.