No it is not relevant. Of course their teams' outputs dropped, they were the two best attackers in the world, how wouldn't it? That has nothing to do with the point I was making. Just look at the tables and compare the highest goal outputs during the Messi/CR7 era with the 90s. Not only Madrid and Barca but everywhere.
And that's only logical as the gaps in budget between the top teams and the runner ups is getting bigger with every year. The concentration of top talent at a handful of clubs hasn't been as extreme in the 90s. And not only that, there are so much more aspects in which top teams have distanced themselves from the rest of the league, like infrastructure, scouting and analytics, medical teams, and so forth. And it doesn't stop here. At the beginning of their primes, we've seen a tactical revolution with the emphasis on pressing and possession football driven by Guardiola and Klopp. It became much more systemized and less negative compared to the 90s. Which is why we've seen a few players reaching previously unseen goal outputs, not only Messi and CR7 but also Lewandowski, Suarez, Salah and Haaland for example. Or the introduction of VAR that saw Cristiano score an unprecedented 12 (?) penalties in Serie A. Plus there's R9's individual situation. In his ptime years that spanned maybe 5 seasons, he switched clubs three times. How did Cristiano do in his first Madrid season? Now imagine R9 who scored 40 in 40 or so for Barca in his debut season despite all the stuff mentioned above growing into his own over 8-9 seasons as Cristiano did, profiting from more and more automatisms, getting to know his team mates better and so forth.
If you really want to compare their goal records, you have to consider all of this. Or, you know, you could stop this silliness and just watch the player and imagine what somebody with such a prodigious skill set could do in the super teams we're witnessing today, e. g. Guardiola's City.