Kennedy probably also won the 1960 election due to electoral college shenanigans. Unlike the Senate which is clearly biased towards whichever party can win the small states, the bias the electoral college gives can benefit either party.
Yes, to me this seems similar to recent Republican gerrymandering efforts that immediately backfired. It’s not a good idea to fiddle with the machinery of elections for partisan gain; it’s likely to have unexpected consequences.
It's always a good idea to remove fiddling whether it benefits your party or not. It's better to win fair without any question of undue gain. The electoral college is one source of fiddling. Gerrymandering and Citizens United are larger sources of fiddling; all 3 should be removed.