MacOS – How to re-download Yosemite for creating second partition

Yep, that's kinda odd. Might be because it needs to partition a contiguous chunk, for efficiency reasons, for Windows. If that's the case, and it's got some immoveable files within that contiguous chunk, I could see it having issues.

I wonder if it would be possible to run boot camp assistant from the OS X disk instead. If you can, those files could probably be shifted as you wouldn't be booted from the 1st partition anymore.

Alternately you could create a bootable partition on an external hard-drive and do the same from a fully functioning OS X installation. Finally, the last resort would be to use a 3rd party utility to add that NTFS Bootcamp partition. I don't recommend that route.

OS X creates the recovery partition as an alternate boot solution for ease of reinstallation and troubleshooting.

It is not needed for normal operation, and as someone that's familiar with boot technology and options, the simplest option would be to simply delete the partition entirely and patch the partition table if needed.

Here is a stock layout:

Mac:~ me$ diskutil list
/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *251.0 GB   disk0
   1:                        EFI EFI                     209.7 MB   disk0s1
   2:                  Apple_HFS Macintosh HD            250.1 GB   disk0s2
   3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3

You could merge partitions disk0s3 into the partition that precedes it (in this case) to effectively erase and then delete the Apple_Boot partition listed as Recovery HD. In this case, you would need to be booted to some other drive than disk0 to have both disk0s2 and disk0s3 unmountable (which would make them disk1 or higher in all likelihood).

 diskutil mergePartitions JHFS+ "Macintosh HD" disk0s2 disk0s3

Should that not work, you might have to image Macintosh HD to another drive as an img file (or straight partition to partition) and then repartition hdisk0 to have just one partition and restore.

As to the deeper question, my guess is that the "hiding" of the partition isn't compatible with other non Apple tools and is confusing the issue - hence the advice to just remove it and count on alternate options to restore your system or boot externally in stead of the recovery HD.