Yeah, two smooth running engines with different tunes should not make any difference. Again only if the engine is not running correctly which I doubt is even the issue in this case. An inconsistent idle can cause it, stumbling, and/or excessively rich condition causing stumbling.
A smooth idle is what makes for a good vac reading. If the idle air control has to keep opening and shutting to keep an idle smooth, that will affect it. Lots of variables.