Where does the coin cell battery sit on these newer Micro ITX boards?

They are often similar to the style used in a lot of laptops, a battery in a shrink sleeve with wire leads and a connector.

Or they could have an edgeways holder - or a conventional flat one; it all depends on the board design.

Search "Wire ended CMOS battery" on google for many examples.

They look like this, often with yellow or blue shrink sleeve.

I don't normally knock questions but,

You could simply do a newegg search and find out by looking at mini-ITX x570, z490, and z590 motherboards. Unlike Amazon, Newegg has a good product search engine.

Find the board you like and then look up a product review for the board.

Here's what I found for the ASRock Z490 Phantom ITX board. With any of these boards, the battery is going to be under the I/O shroud.

They're not all in the same place. You'll have to specify the model you're talking about if you want an exact answer. On gaming motherboards, they're often slapped to the side of an Ethernet or Wi-Fi antenna jack and connected to the motherboard with a pin header.