Let's take this to its logical extreme.

There are two seats in the back and one jumpseat available.

The standby list looks like this:

UAL Pilot
UAL Pilot GF
Other UAL Employee

The jumpseat list looks like this:

The same UAL Pilot
You, an offline jumpseater

So, the UAL pilot can take either a seat in the back or take the jumpseat. Remember, there are only two cabin seats left.

If he takes a seat in the back, him and his girlfriend get on, and because he has a seat in the back, you get the jumpseat.

If he takes the jumpseat, his girlfriend and the other UAL employee get the seats in the back, and you get left behind.

See how this works? Maybe he hadn't paid attention to how much space was left, maybe things changed, I don't know, and it doesn't matter. Him letting you know he was taking a seat in the back was to assuage any concern that you might have had, not knowing exactly what either list looked like, that he might be bumping you off the jumpseat. It's a common professional courtesy that is practiced all across the industry.

The fact you seem to be insecure about it and making the least-respectful interpretation of it says an awful lot about you.