Caching has nothing to do with disk alignment. It sounds like your sysadmin should have gone to my SQL PASS pre-con. All the caching does is accept the writes from the host into D-RAM instead of writing to the disk directly.
Now if the LUN is aligned on the array by setting the offset on the array side (which isn’t recommended as it makes LUN migrations within the array more difficult) then you want to leave them misaligned in Windows. If however they are setup with a 0 offset within the array (which is the default) then they need to be aligned within Windows.