For pure stains/dyes, alcohol/spirit or water is only the solvent used, the dye/stain itself is basically the same fine powder. So once the solvent's evaporated, there's really no difference in the result and you can put exactly the same stuff over it.

I find spirit based stuff easier to work and blend, though it has less surface tension and gets into small cracks in binding a lot easier than water based stain does.

But some stains do have a 'fixer' element, basically a varnish, that will lock them in place once they dry, so that can limit some of the finishing options, especially when blending or when re-staining areas.