He's calculating EV above cost. If you look at the calculation, the first term is -1000 to account for the initial investment. So the final value is tell you that you got back the initial money plus 900 more.

However, the article is technically inconsistent in framing.

The calculation that arrives at 900 has already subtracted the 1000 from the start.

it's correct. the EV is 900 after accounting for the 90% probability of -$1000. that's what the first term in the sum is for.