Their terms are that you can't sell *Steam keys* for cheaper than the game is listed for on Steam.

There is a class-action lawsuit on this that's been ongoing for half a decade now, but as far as I can tell the plaintiffs have not been able to produce any actual contract text supporting this claim. The closest their filings come is some random customer support rep.

I wonder how the terms of that work exactly in practice. For example I'm pretty sure Humble Bundle includes games that are on Steam every now and then, with a pretty solid discount if you consider what you get for your money.

In practice it means Steam reviews the key requests you make for third party bundles and sales. If they decide the deal is too generous, they may deny the key requests until you've offered the game for a comparable price on Steam.

Mindustry is paid on Steam but free on Itch.

Really? I've noticed a few games that are cheaper via apple's app store than they are from steam. It's not a big difference, usually ~$5.

Is there a steam version though? I don't see it on there

It's mentioned as upcoming in the FAQ under "How much will it cost?": "$30 on subwaybuilder.com and $40 on Steam (page is coming soon). The Steam launch won't happen for a few months after the launch on subwaybuilder.com."