Pretty sure I had this right but thought I'd check.

Somebody suggested that since Mandatory Upgrades does not specify a trigger (such as score/stolen), when stolen by the Runner it would give them an additional click to spend.

The core rules say that agendas are active when in the Corps score area, but nothing to this effect is mentioned under the Runner's rules (they get the agenda points and that should be it). Similarly no Runner double clicking Gila Hands for money.

I've always assumed agendas were *only* active in the Corps. score area (on access effects not withstanding). Giving the runner a free click (or two) to play with just for stealing a 3-point agenda would just add insult to injury.

You are correct. Any benefits (unless explicitly stated on the card) of Agendas are only active when in the Corp's score area.