If they set it to 1080-59.94i and AVC-Intra50 at 60i, then that means you will be recording 1080/60i footage, an HDTV standard. It will be interlaced, and the motion will look like "real life".

If you set it to AVCI50/30pN, then that means you will be recording 30 progressive frames per second. It will look more filmlike, and will not be interlaced. It won't look like "real life", it'll be a bit more surreal, more filmlike, with stuttery motion on wide pans and such.

If your head office has declared to go with 60i, then I would go with 60i...