Yes, the M/E rating is combined with the CPL skills test. As you correctly point out, the main difference with doing it in a multi is that you'll have to deal with asymmetric flight instead of PFLs. Anecdotal evience from instructors I've met suggests that more people trip up on PFLs than asymmetric flight, so in that respect the skills test may be slightly easier in a multi. If you already have 40hrs M/E then you should have no problems coping with asymmetry.
I did my CPL in a Duchess, and it made for a much easier transition to the IR. The IR is incredibly hard work, and much of it will be completely new (e.g. airways, holds, instrument approaches). You will do yourself a big favour if you're already familiar with flying the aircraft to CPL test standard, as it's one less thing for your brain to have to deal with.