This shouldn't be the case, I was testing this just yesterday and confirmed that Mega Drive/Genesis 1:1 PAR worked correctly, even for 240-line PAL games. Which setting are you using under aspect ratio? There should be one which gives an aspect ratio, then in parentheses, "1:1 PAR". This one should just detect the resolution the core is feeding it and adjust to match the title. The aspect ratio before the "1:1 PAR" will vary depending on what is running.
The only core which doesn't yet support this functionality from what aliaspider said is CatSFC, which is just hardcoded to 256*224 (Snes9x-Next functions as expected). A handful of games run 239 lines rather than 224, but it's few enough that generally you'd probably never even notice the issue.