Why does this picture of Ross look like some weird Mandela Catalogue pic...

While I agree that pair programming doesn't fit everyone and all situations. Especially as a developer gets more experience, or for things that could be considered "scut work". What you're describing here really doesn't sound like effective pair programming.

One person shouldn't be just "watching" the other program. Especially for extended periods of time. There should be some regular interactivity or collaboration. I have found things like the "driver / navigator pattern" helpful.

As mentioned Aseprite has a linux build.

Pixelorama is very similar to Aseprite, but has free builds. Is built with Godot and is open source.

It looks like Aseprite can export a texture atlas, but I haven't seen the ability to do so in Pixelorama.

For lighting effects there's an application called Sprite Lamp (also has a linux build) that's been around for a long time. I haven't used this one though.

I haven't done any of these workflows in awhile but I hope that this helps.