Engine mapping differences for qualifying and the race, at least at Indy, is something I've thought about before as well. I don't see the downside although I do see the need to keep the genie in the bottle somewhat. They can't be finding an extra 10MPH each year or else they will outrun advancements in safety.
OTOH, hamstringing the cars until they are running speeds they ran 20 years ago isn't the right answer IMHO.
Once the genie was out of the bottle and the 240MPH barrier was in sight (239MPH in practice... 236MPH qualifying), following that the next year with 218MPH wasn't exactly stupifying for the public's imagination.
They did get over the 230 barrier again in 2002 and 2003 but then went back to 222MPH in 04.
There has always been tweaks to slow the speed increments down over the years, but during the IRL era they've been much more active in keeping speeds down.