I have used spirit based stain on my rcA 4 kit, no issues with the different take up of the stain on the different timbers, I used a black stain on the back and neck, amber on the headstock and front of body.
If you apply the stain with a rag and don't mask the binding, you can apply it avoiding the binding by using a small rag folded carefully. That way you should avoid the problems with it seeping into the binding. If you mask the binding and rub the meths stain across it whilst staining it tends to creep under the tape and into some cracks and faults in the binding where it shows up as a line. As Simon says I'd imagine it's to do with the viscosity and surface tension of the spirit based stain.
Any stain that ends up on the binding can be carefully removed with fine steel wool or a scalpel blade gently scraping sideways across the binding as you would a knife across hard butter.
Then you can clear over the stain, covering the binding with clear too or masking it off.