Assuming he didn't do 'roids (you're right that I don't know whether he did or not), my thinking is that the '93 expansion would have had more of an effect on the NL than the AL. The former got two new pitching staffs; the latter might have lost the 23rd and 25th players off their rosters. Again, assuming O'Neill was clean, many of the pitchers he faced were not, and meanwhile he had to compete with all the juiced hitters.
I actually think you're onto something that the '93 and 98 expansions played a bigger role in the offensive surge of the 90s than people acknowledge. Everything is blamed on juiced hitters, juiced balls, and juiced ballparks.