I'm not sure I agree. One counter argument would be that topic-specific instances are significantly more likely to have performance issues and downtime. The benefit of having communities on larger, general purpose instances is that the major instances are more reliable and trustworthy that they will still be up a year from now.
For instance, I was quite active on lemmy.beyondcombustion.net. That instance no longer exists, and the small but growing community of vaporents on Lemmy was disrupted by that event.
You're not wrong that it's a bit more confusing to have things scattered around like this, but imo it's a worthy sacrifice, because the actual functionality is better. If the communities are actually good, people will find them. I think having multiple entries is fine, as long as it's clear which one is the most active.