It's a prototype, the red light boards give it away. Different inserts sometimes are also a common difference. Printer interface boards are not common in production machines, but some operators used them for audits.

Prototypes are desirable to some, but unless their were additional game features not available in production games, this does not mean the game is made "out of gold".
Who Dunnit is B title game that is not overly collectible, although still fun. The machines looks to be in good shape, so that's a perk.

Non permanent mods is not going to change or hurt the value.

"Sometimes", but not necessarily.
Dependent on the timing started for production. Sample games were rebuilt with standard boards if problems were identified, or if features were changed or removed. Otherwise, yes, they were sold out to operators or provided at discounts for support of testing.

Sample and prototype games many times are the same thing, as they were used for the same purposes after creation. Meaning protos turned into samples "on the route" for testing.