Just my personal take on this ... not official:

Manufacturer samples are the chips with various chip makers' names on them. GPI, Paulson, Langworthy, etc. There's a whole group of them on the Chip Guide. Frequently handed out at trade shows. Used to show technical abilities and anti-counterfeit features available for purchase.

Prototype chips are made specifically for a casino, to show color combinations, artwork, check for surveillance cameras to read them, etc. They may go into production, or not. If not, they're usually rare, with only a few made. May have unfinished edges or other signs of being a prototype.