Why does every color in my design turn into a separate job layer?

You're not missing anything obvious, the toggle just isn't where you'd expect it. In BeamSketch every color is its own layer and each layer row in the settings panel has an enable checkbox (or eye icon, depending on where you're looking). Untick the grey text layer and it stays on the canvas with your positioning intact, it just gets skipped when the job runs. No need to shove stuff off the canvas like that.

Same trick works for the cut layer, obviously, so you can flip it the other way and only engrave the text if you ever want to. The nice part is the layer stays visible on screen, so when you hit frame you still see the full footprint of the design and can line it up on the sign blank properly.

On the export side, yes, it behaves differently. When you send over USB the software streams one pass per layer, but when you export the GCode file it bakes everything in, including the passes count from each layer's settings. If a layer is set to 2 passes, the exported file will contain that line twice. So if you saw multiple passes on the same geometry, check the passes field on the layers you didn't think you'd changed, some of the defaults are set higher than you'd guess for a low power diode. And the disabled layers, last I checked, still get written into an exported file, so double check that before you save it. If the checkbox trick doesn't survive the export in whatever version you're on, making two files is a fine fallback, just keep the master file with everything in one place so your alignment stays consistent between them. That's what I do for anything where I want cut and engrave settings dialled in separately anyway.

That export thing burned me too. My fix is to open the exported file in a plain text editor and scroll through it before it goes anywhere near the machine. You can literally see if a line got repeated or if something you switched off snuck in. Takes ten seconds and saved me a few ruined blanks.

One thing I still don't get is why the defaults are set so hot for diode machines. First week I had mine I scorched a piece of ply thinking one pass at the preset was safe. Ended up making my own starting settings and saving them, never touched the presets since.

Glad I read this far down becasue I've been doing the two-file thing for months and assumed that was just how it works. I make cutting boards with a mate's names engraved on them, so one file for the engrave and one for the cut, and it's been fine except I'm always paranoid about the board shifting between jobs. I draw a little corner mark in both files and line up off that, which is probaly a crude version of what the checkbox method does properly.

One thing I'm still fuzzy on though, if I keep a master file with everythign on it and export both files from it separately, do the coordinates stay matched up between them? Or does each export recalculate where zero is based on what's enabled? Because if it's the second one my corner mark trick has been a waste of time.

I'd push back on the 'keep a master file with everything in it' advice. I did that for months thinking it was the tidy way, and it nearly cost me a nice sheet of ply because I forgot one layer was still enabled when I hit go. The toggle got flipped back on at some point and I never noticed. Now I strip the file down to whatever I'm actually running before it leaves the editor. Extra work maybe, but I'd rather delete and re-import than trust a checkbox I can't see the state of when the job starts.