1) Yes. I tried to imply this with the misplaced shot wounds on Dr. ████████, but this probably wasn't made clear enough. I'll attempt to clarify that.
2) That's a very good point. I'm now trying to figure out if that would work, but due to a rather limited understanding of chemistry I'm not doing too well. I guess it would be neat to mention details like 'lemons smelled of oranges' (due to limonene) or something like that, but how big would the effects be? Would the appearances or functions of things change drastically? If it does, then the mirror stops being so neat. I'd also not be too sure of what I'm talking about, so it might have to be limited to either the sedative being specially synthesised, as you say, or the researchers being reluctant to give the doppelganger anything chemical because of uncertainty as to how it would affect them.
Another alternative is that the chemistry is mirrored, but due to magical mirror effects everything acts no differently to the normal world. Although then I'm not sure how you'd realise that the chemistry was mirrored. I think that probably works best, actually. I'll add this.
And thank you! I don't think that would have occurred to me if you hadn't pointed it out.