Costs for staff are not just salaries. It's also pensions, taxes, benefits, the offices, software licenses and all the other stuff. I've often heard 50% of total cost going to salary, but it varies.
Pensions aren't a thing in the U.S. anymore, especially not for tech. And when a U.S. company says "staffing costs" that does not include licenses, offices, etc. It's strictly salary and benefits.
According to Signal's 990, it's paying multiple employees over $700k. That's above-market for corporate compensation, and it's way above market for non-profit compensation, to the point where it could be considered private inurement.
They cover this pretty substantially in the post on Signal's website (I know they merged the Wired article into this one).
Signal is trying to compete with the richest companies in the world; including for talent. And considering Signal's origins and motivations, they're not going to lower salaries or decrease benefits because some people believe that working for a non-profit automatically means lower compensation.
Engineers doing the same work on iMessage and Meta Messenger, i.e., their direct competitors, make less than 660k/annually in salary and benefits.
This means that the pay packages are likely not based on comparable market wages, which is an actual legal requirement for highly compensated employees for U.S. charities.
Still does seem high though.