The alcohol is what caused the color to get impregnated into your wood fibers. It dissolved the residue, and then got wicked into the wood fibers, premanently impregnating the wood with the color.
It sounds to me like you may not be using proper masking tape for the job and also that your technique for applying it may not be quite there. What you are seeing is what happens when the tape isn’t fully adhered to the material and there’s a small gap for the smoke to get under and stain your material.
You should take a look at these posts:
A tip on material prep:
Where to get proper medium-tack masking, #2 on this list:
On the importance of properly pressing down on masking:
My preferred tool for pressing the masking:
And lastly, I don’t believe you’re seeing flashback on your material in that living hinge cut, I think the masking is protecting it properly. If you’re wildly overpowering the cut you will flash back hard enough to cut through your rear masking and damage the surface; that looks undamaged, simply smoke-stained as in the case where your masking isn’t properly adhered. You certainly aren’t seeing flashback on the engraving, since that doesn’t even cut through, you’re never talking about the back of the material there anyway.
All might not be lost though, if you get some smoke stains on raw unfinished plywood like this my advice would be to lightly sand with ~220 grit sandpaper, the surface staining will come right off.